As ABC Family has renewed the U.S. television drama Kyle XY for a 23 episode second season,^[1][2] episode information will go here as it becomes available. Kyle XY Season 2 premiered on 11 June 2007.

On May 3, 2007, ABC Family extended the number of episodes for the second season from 13 to 23. ABC Family President Paul Lee says, "We have been delighted with the new episodes, and we're thrilled to be able to extend season 2."^[3]. The second season will be split up into two halves - one of 13 episodes to finish airing on September 3, 2007 and one of 10 episodes to air in early 2008.^{[citation needed]}

At the Trager house Nicole wakes up to a bad dream about Kyle being in danger. Adam Baylin welcomes Kyle into his home and offers some answers. While offering Kyle a drink of water he moves the cup with his mind and explains to Kyle he is able to do the same with training. Adam explains the origins of where he came from, what Zzyzx is and what Latnok means. Nicole and Stephen decided to take a weekend vacation to San Francisco and leave Lori and Josh home alone. Adam explains to Kyle how he was created and why he has no belly button. Josh decides to throw a party in his parent’s absence. He briefly talks with Kyle through a web cam while the party is on-going but cuts the conversation abruptly short. At Adam’s house Tom Foss warns Kyle that his conversation with the Tragers almost lasted past the two minute mark where Zzyzx can trace the connection. Tom advises Kyle to cut off all connections to the Tragers.

Outside Adam collapses but his trusted friend Brian Taylor is there to assist him. Adam explains that Brian brings Adam’s useful ideas to the outside world and Tom protects Adam from Zzyzx. The next morning at Adam’s house he continues to train Kyle. Nicole and Stephen return from their weekend trip and find proof that Josh had a party while they were away but, did not punish him. Kyle begins questioning Tom about Zzyzx and why he never bothered to ask questions about what was happening. Tom simply explains he was doing his job. In Lori’s bedroom Declan and she are making out but she senses something is wrong with him; most likely related to Kyle leaving so abruptly. Lori suggests Kyle come visit but, Declan quickly states that he is not coming back. Through the web cam Lori and Declan ask Kyle about Connecticut and his parents. Lori wants Kyle to fly out to Seattle. Kyle suddenly hears Adam collapse and runs to help him leaving Lori the impression he does not want to visit.

Adam finally explains to Kyle that his body is failing and if Kyle does not condition himself he could die young. Suddenly Kyle remembers the timer and cuts the connection but, the two minute mark has elapsed. Having trouble dealing with Kyle’s absence Nicole begins to see a therapist. Dinner time at the Tragers but there is no dinner because Nicole has stopped cooking for the family despite having a huge amount of free time because she quit her job. Josh questions Stephen about not punishing him for the unsupervised party. Lori mentions she invited Kyle to visit but Stephen believes it is best to cut off all contact to Kyle in order for everyone to move on. The next morning at Adam’s house Kyle begins to question why he is there and why Adam created him. Adam explains he was lonely and wanted someone else like him in the world and asks Kyle’s forgiveness. Kyle concentrates on the glass of water in front of him and shatters the glass. Suddenly a shot rings out and Adam is killed by a sniper. Tom comes to his aide but Adam is already dead. At the bank of a river in the forest Kyle spreads Adam Baylin’s remains.

While returning to the house he walks in on Tom and Brian arguing. Tom wants to eliminate Zzyzx in order to protect Kyle but he does not want Tom to harm anyone. While checking for any messages from Kyle, Nicole questions Josh about Kyle. Josh confronts Nicole about her ignoring him since Kyle has left. Tom enters Zzyzx with multiple bombs. He begins planting them throughout the building and enters a room with a female inside a liquid chamber. The chamber is labeled XX. Tom spots Kyle on a security camera and comes up from behind and knocks Kyle unconscious. Outside Zzyzx Kyle awakens and the bombs explode. Tom and Kyle argue at the house about why he had to harm anyone. Tom explains why he had to attack Zzyzx and advises Kyle to keep learning what Adam taught him. In the living room Nicole tells the family she would like to cook dinner and punishes Josh for throwing an unsupervised party. In Adam’s house Kyle explains to Tom that if he is to touch the world he must be a part of it. Kyle does not simply wish to be in a safe shut-in environment for the rest of his life. He wants to return to the Tragers because he loves them.

At night Tom drops Kyle off at the Trager house where he is warmly received. The female inside the chamber labeled XX inside Zzyzx has somehow escaped and is walking nude with a liquid substance covering her body to the city.

Kyle yearns to return to the warmth and love of the Trager family, but he is forced to explain his sudden presence with a web of lies. His commitment to leading a double life places him at odds with Declan, the only person with whom Kyle had previously been completely honest. Kyle struggles to find a balance between the normal life he wants for himself and Adam Baylin's vision of who Kyle could be. Meanwhile, in the woods outside town, Kyle's podmate XX wanders naked and covered in pink goo (just like Kyle had done in season one). However, unlike Kyle, XX is soon traumatized by a violent encounter with a camper, who she quickly kills. The CEO of Madacorp (the mega corporation behind the Zzyzx experiments) takes a personal interest in recovering XX, who he considers to be property of the company. He sends Emily Hollander, a creative and resourceful agent, to recover XX. When Emily locates XX, she discovers a portrait that XX had drawn of Kyle. Recognizing that Kyle must still be alive, Madacorp makes recovering him priority number one. At home, the Tragers unanimously decide to welcome Kyle back into their family.

Kyle's attempt to return to a normal life at the Trager's house is complicated by Tom Foss' training. Meanwhile, Jessi (XX) begins her mission - to get close to Kyle. Kyle and Amanda meet. She has heard about Kyle's parent's "death", and gives him the charm of the patron saint for those who have lost a parent. Kyle contemplates telling the truth about Charlies cheating ways to Amanda but is interrupted by him. He also must make trips to train with Foss, where he is learning to use his mind to control his body temperature ("mind over matter"). Lori and Hilary decide that they want to "revirginize", seeing as all of their troubles began once sex entered the picture. Once they realize that they do not really know what else to do with their lives other than think of boys and sex, they decide to consult a virgin. This brings them to Amanda, who is working on the bonfire committee. When they tell Amanda of their plans to revirginize, Amanda asks them if they thought sex was a mistake; Amanda seems a bit uncomfortable. She tells Lori and Hilary that, since it's her and Charlie's two-year anniversary, she thought that maybe it was time to lose her virginity. Hilary and Lori are shocked and tell her that this is a bad idea, but do not want to tell her why. Lori then calls Kyle during his training with Foss. When Kyle hears, he leaves immediately, tell Foss that he does not want to change the world; he only wants to be ordinary. Kyle then gets to the bonfire, where he considers telling Amanda about Charlie. Declan and Lori talk, and Declan breaks up with Lori. She is emotionally torn apart, despite telling him that he has been erased and they "never happened" (after revirginizing, she has erased their sex as well). Meanwhile Charlie is talking to a new girl, who goes to the sex shack to wait for him while he "sorts something out". Then he confronts Kyle, but Kyle gets distracted. Jessi has somehow been brainwashed. she believes she is Emily Hollander's younger sister, and is a new girl trying to blend in and make new friends. Jessi is on the other side of the bonfire, and she and Kyle can both sense each other. But Charlie pulls Kyle out of his reverie by yelling at him, and Jessi is bumped by another teen. The boy apologizes and touches her arm, prompting her to subconsciously remember the man in the forest who assaulted her. She then begins to choke him, but Emily Hollander comes and gets her to stop. They then leave the bonfire - fast. Charlie then confronts Kyle, asking him what the heck he is doing. Charlie wants to start a fight, but Declan comes and breaks it up. The three begin to argue, but Kyle senses a fire. Some sparks from the bonfire ignite a propane container, setting the shack on fire with the girl inside. Charlie leaves to get help, and Kyle enters the shack and pulls out the girl, who has passed out. Kyle's clothes are set on fire, and Declan puts them out, but is astonished when he sees that Kyle has not been burnt. Sirens are heard, and Declan tells Kyle to run away. Kyle runs into Nicole before he can leave. He looks at her guiltily, then runs off. Later that night, Kyle and Nicole talk about Kyle's extraordinary abilities. Kyle tells her that he does not fully understand them and that he does not want anyone to find out because he might be forced to leave. He says that he just wants to be ordinary. Nicole reassures him and says that he could pretend there was nothing abnormal about him, but when a girl needed help, he rushed into a burning building to save her, and there is nothing ordinary about it.

At the school, an annual list of students was compiled, best couple, biggest slut, etc. Charlie was named biggest slut, dethroning Hillary from the previous year. Amanda is shocked, with Charlie saying it is a joke. Hillary explains it is not joke by telling Amanda that she slept with him. Amanda runs off in tears, with Charlie giving Kyle a gazing stare. Elsewhere, the best couple named: Lori and Declan. Lori, downhearted, says that this just proves how wrong it can be.

At the end of the episode, Kyle reminisces about the happenings of the past few days. He says that everyone is given a label. Charlie was a cheater, Amanda was the betrayed, and Lori and Declan, the heartbroken. He himself must face himself and stop running away from his label: extraordinary. He then approaches Tom Foss and tells him that he is ready to face his destiny.

Kyle has been sneaking out every morning at 4:30 to run a rigourous workout with Foss to strengthen his body so he can use his abilities without harming himself. By the time his morning workout with Foss is complete, the Tragers are just getting up. Kyle learns that by doing this every morning he will eventually get caught, and making his two lives work is going to be a lot harder then he first thought. Josh passes his drivers test and tries to cash in on the deal that his father made with him, buying him a car for his birthday. Everybody goes about their morning routine, and it is learned that Stephen's company has been sold and he is now out of a job. Nicole and Stephen talk about what their options are and decide that they will not tell the kids until another job is lined up. Back at the coffee shop, Kyle tries to approach Amanda, but she is still upset with him. Lori tells Kyle to give Amanda some space, and Kyle asked Lori if that is what she wants from Declan. Her response is that she wants an explanation and she can't stop thinking about it. Kyle explains that she should find an activity on the activity board. She decides to take up guitar lessons. Meanwhile, Josh and Andy J are looking at girls and pointing out which kind of car would impress them. Kyle makes it look like he is reading a book, while watching Amanda. She notices and approaches him. She asks him what he is doing and he replies "giving you space." she answers back "No! You're staring!" He says that he wants to say one thing, but she says that she's not ready to hear it. Right after Kyle receives a text from Foss which tells him that he is late for his workout, which he rushes off to. Josh is hurt by this, as Kyle said that he would look at cars with him after school. Foss and Kyle argue about what Baylin's research was meant for. Foss simply tells Kyle that Foss can give him the conditioning that Kyle needs. Eventually Kyle lashes out at Foss. Foss tells him that he was in a recon unit and explains that it is short for rescue and torture. Kyle asks which one was Foss trained for. Foss explains a few moments later that his family was killed by a drunk driver, and that Foss stays at an old abandoned warehouse where Kyle trains. Kyle tells Foss that he can call him whenever he needs, or simply text three stars. Kyle comes home late, and is confronted by Nicole about breaking curfew, and tells him to get rid of his burnt clothes from the fire if he doesn't want anybody to know. When Kyle leaves his cell phone rings on the table, Nicole looks at it and it simply comes up as T. She answers and Foss hangs up.

The next day Nicole is walking down the street focusing on her phone when Emily bumps into her and spills her coffee all over her coat. Emily states that she recognizes Nicole from a lecture, and that she was great. Nicole says that she will pay for the clean up of the coat. Nicole and Stephen argue about a car for Josh now that Stephen has lost his job. They talk in code so that Kyle will not realize that Stephen has lost his job. Kyle picks up on it right away, and Stephen is glad, because he is sick of living the lie. Stephen feels bad because he does not want to break promises like his father did. Kyle tells him that he is a great father. Lori and Declan bump into each other after one of her lessons. She tells him that if he still cares about her, he can come and explain what happened.

Foss listens to a news report about the man that Jessi killed, and it spooks him. He makes Kyle come in even though Kyle is suppose to have weekends to himself. On his way out he sees Josh in Amanda's car just checking it out. Kyle and Amanda share a couple words. She says "Being someones friend isn't about what you should've done, its about what you do." Kyle says "I know you're hurt, but you always look for the best in people... Never lose that," and he walks away heading for his training with Foss. Declan is about to visit Lori when he sees Kyle running off. Instead of going to Lori, he follows Kyle.

Josh is told by his father that he won't be able to get him a car. Emily goes to the Trager house. There Emily is able to convince Nicole to talk to Jessi, saying that she had a tough childhood. Emily makes a phone call and tells the person on the other end of the line that Jessie has a therapist.

Foss makes Kyle scale a wall that would be impossible for any normal person to climb. Kyle tells him that he is not ready for it. Eventually Foss tells him that he isn't ready for "the jump...yet" and that he will allow Kyle to work up to it. Kyle heads off so he can go to Josh's birthday dinner, Foss is readjusting the wall so but falls over the edge. He is hanging one with one hand and texts Kyle three stars with the other. He sees the Tragers getting in the car when he receives the text. He makes the decision to go back to Foss. He makes it just in time, and makes the jump that he couldn't make before to save Foss. It is learned that Foss was the drunk driver that got his family killed, or it was his fault that his family got killed. Kyle tells Josh that he was sorry that he didn't make the dinner and that Josh wasn't going to get the car. Josh, very upset, tells Kyle that the car wouldn't have been a big deal if he still had his best friend.

Kyle is confronted by Stephen and Nicole. They believe that Kyle does not want to live with them, because they believe that "T" stood for Taylor, his "attorney". Kyle tells them both that even though he was been distraced, he didn't want to give the impression that he didn't want to stay there. Nicole tells him that they want Kyle to be a part of the family, but Kyle needs to feels the same. Kyle reassures them that "nothing is more important to him." Stephen talks to Kyle. Stephen tells the story of his first car, and how it was a Junker and that it would be the perfect starter car for Josh. Kyle tells him he knows of the perfect car. Kyle and Stephen give Josh the car and Josh loves it. Andy J goes to Josh and gives him fuzzy dice for his rear-view mirror. Josh asks her what kind of girl could he get with that car and she explains "The kind who appreciates potential." Kyle sees Amanda get out of her car, she looks at him, he waves. She smiles and waves back.

Lori practices the guitar, which fascinates Kyle. He tries it and realizes that each string and each fret had a particular sound. He compares it to math, and figures out that its all a matter of putting the pieces together. He plays a song and Lori is impressed. She says that the guitar is theraputic, and that it has been helping her with life after Declan. Meanwhile Declan enters his car to find a large envelope. In it are pictures of his car, the warehouse where Kyle trains, Declan peering through the windows, and finally a picture of Lori with a black X through it with a note warning, "BACK OFF IF YOU CARE ABOUT HER."

Kyle learns that "We all struggle to find the right path to take in life. It's not always easy to know where that is or where it will lead us. In the end it's the people in our life that give us the balance to make it through."

Coming back to work, Nicole has a startling new patient: Jessi. Jessi was recommended by her "sister", Emily, because Jessi supposedly had a rough childhood (Emily told Nicole that their parents abandoned them when they were young, and that Emily has had to raise Jessi. This has undoubtedly scarred Jessi, and she is having trouble coming to terms with it). In truth, Jessi has been sent on a mission: get closer to Kyle. Since Jessi's therapy sessions are to be held in the Trager home, Nicole tells everyone to stay clear of her office, reminding them that everything she does with her patients is confidential. However, when Jessi enters, Kyle senses her, just as she senses him. Kyle gets up from his drawing and walks downstairs, as if he is in a trance. He then proceeds to the door of Nicole's office. He then listens at the door. Jessi, sensing Kyle, is uncomfortable, and tells Nicole that there is someone there. Nicole assures Jessi that there is not, but Jessi insists that Nicole check before they begin their session. Kyle hears this and is gone by the time the door is opened. At the end of Jessi's session, Kyle is nowhere to be found. Declan, who has come to pick up some things from Lori, walks down the stairs. Their relationship is officially done since he didn't show for Lori's little "meeting". As Declan is leaving, he drops many of his items, and Jessi helps him pick them up. However, she doesn't give him her name until he is almost gone, because she has an instant crush. Declan notices this and smiles. Lori, who has been spying from the stairs, turns away in disgust.

Meanwhile, Kyle's mission is to find Amanda's stolen bracelet. After a break-in at Amanda's house, she discovers that a very valuable bracelet is missing. It's extremely important to her because it was the last thing her father ever gave her before dying. She doesn't care about it's monetary value - just her dad's memory. Kyle sympathizes with her because he feels the same about a mysterious ring. Amanda asks if it was given to him by his family. Kyle, thinking of Adam Baylin, says yes. Kyle and Amanda are called into the police station to help identify the robber from a number of suspects. Kyle helps by identifying the car. However, he didn't see the face of the criminal, so he can't help in identifying him. However, when they all leave the room, Kyle recognizes the abnormal heartbeat of one of the suspects. Knowing that he has already told the police he didn't recognize the man, Kyle must act on his own. He narrows down the next likely house the man will rob, and then he and Lori stake it out. When the man comes, they report the robbery in progress and catch the thief. However, he doesn't have the bracelet. Assuming that he pawned it off, Lori and Kyle visit various pawn shops until they find it. They tell the owner that the bracelet was stolen several days ago, but he says that the bracelet has been there for weeks. Kyle and Lori, confused, look at the log book. It says that the bracelet was sold by Amanda's mother! Unsure of what to do, the two leave, but Kyle returns soon after. He trades his ring in for the bracelet.

Kyle goes to Amanda's house with the intention of speaking to Amanda's mother. He lets her know that he knows that she pawned the bracelet, and gives her the opportunity to give it back to Amanda, pretending that she just found it in the house. Amanda however sees Kyle with her bracelet and asks how he found it. She is happy at first, but soon realizes that there is something more to the story. She asks both Kyle and her mother what's wrong. Her mother politely asks Kyle to leave so she can speak with her daughter. Later, Amanda talks to Kyle, saying that since her dad died, her family has had money problems. Her mother had to sell the bracelet to support Amanda. She then gives Kyle an envelope with money in it, saying that he can buy his ring back. Kyle doesn't want to accept it at first, but he then agrees. However, when he reaches the shop, the ring is gone. the owner says that the man who bought it "payed him a lot of money to lose the receipt".

Stephen attends several interviews, and is offered a job at a high-tech company. He is shown shaking hands with the man from Madacorp (the company that ran Zzyzx), who is wearing Kyle's ring.

• This episodes features a reference to the CW network series Veronica Mars, with actors, Enrico Colantoni and Kristen Bell, to whom, earlier in 2007, Matt Dallas presented the Family television award for favorite Father-Daughter team.

Visions take over as Kyle’s powers become more sophisticated and pop up in the most inappropriate places. He’s standing in the local hangout, The Rack, when the words “Viz Allati” (víz alatti is Hungarian for the adjective “underwater”) come to him. Kyle feels an earthquake right before it happens. Intrigued, Foss and Kyle hunt through Baylin’s records to find the meaning of this message. There Kyle discovers a book covered with fish that hides a data disk inside. When Kyle deciphers the message, he’s shocked to see it reads "Don't Trust Foss." Right before Kyle figure out the message, he received a message from Foss telling Kyle he is leaving town for a while. When Kyle goes to the warehouse, everything is gone; everything that had something to do with Foss. Its as if Foss was never there. Josh prepares for his first date with a girl from school with help from Andy. However, at the end of the night, the girl stands him up, thus Josh and Andy go on the date together. Lori prepares herself to play the guitar during an open mic night. She writes a song about Declan. Declan, however, is too interested in Jessi to notice that Lori is up on stage, and walks out as soon as she begins playing. Jessi and Declan kiss. Amanda and her mom are in extreme debt, so to cover some of the debt, some of Amanda's sacrifices were to give up her piano and her car. Kyle learns about this, and finds a piano in an alleyway. He brings it home, and cleans it up so he can give it to Amanda.

After Kyle gives Amanda a refurbished piano, Amanda asks him to a school dance. He initially does not think that Amanda considers this a "date", but Lori quickly convinces him of the opposite. Kyle is subsequently confused by his own anxiety about the date, and Nicole helps him understand his feelings. Plans to attend the school dance are soon derailed; Kyle, Amanda, and several friends are banned from the function after they engage in civil disobedience to protest the school's discrimination against gays and lesbians. The controversy reveals Josh's discomfort with homosexuals, and Kyle tries to help him see things from another angle. Kyle enlists Josh's talents as a dance instructor; this new activity is challenging for Kyle and progress is slow. Despite her mother's disapproval, Lori befriends Jessi; at first, she merely wants to keep a close watch on Declan's new girlfriend prospect, but she becomes sympathetic to Jessi as they spend more time together. Lori also takes steps to make peace with Declan. Declan drags Charlie to the alternative dance to support Lori, because he feels guilty for recently abandoning her during her open-mic night performance. Charlie's homophobia is evident in his behavior at the dance, which leads to a confrontation between Charlie and Declan. Josh is relegated to clean-up crew at the dance after he steals ("borrows") a radio from a dead student's car; however, his mom allows him to take a break to dance with Andy. Amanda, who is grounded, sneaks out of her house so that she does not miss her date with Kyle. They dance together, and Kyle takes a turn dancing in sync with Josh in the center of the room. Jessi becomes concerned that Lori and Declan may still have unresolved feelings for each other, and questions them both on the topic. Amanda and Kyle dance closely and almost kiss, but they are interrupted when a distraught Jessi unwittingly triggers an electrical malfunction. The dance ends early, but Andy kisses Josh on the cheek and Amanda kisses Kyle on the cheek. Kyle and Amanda agree that they both want to go on another date together. Outside, Kyle and Declan address their falling out; Kyle tells Declan that he wants to finally tell him the whole truth, and Declan tells Kyle that he is ready to hear whatever he has to tell him. Declan declares himself to be committed to his relationship with Kyle, and their search for the truth. He then shows Kyle a threatening message that he had recently received from Foss; the message indicates that Lori will be targeted if Declan does not stop asking questions. The episode then ends with Lori getting knocked out by someone unknown while she is tossing out the trash.

Lori is back at home recovering from her injuries following the attack in the alleyway. No one knows who attacked her or why; however, Declan suspects Tom Foss. Everyone is acting a bit different around Lori, which she doesn't like, but at the same time she doesn't show signs of really being emotionally affected by her attack. Jessi continues her sessions with Nicole, who suspects that Emily isn't as she appears since Jessi seems to be afraid of her at times. Nicole tells Emily that she wants to continue seeing Jessi and that if she doesn't she will contact social services. This causes Emily, who is missing her daughter Paige, to want to resign from her job, but her boss convinces her to just bring Jessi in as she has a "glitch." Jessi manages to figure out that Nicole believes she "lacks empathy and socially manipulative and feels no remorse", causing Jessi to feel depressed, as she is unsure why she does the things she does. It is revealed that Jessi was Lori's attacker and that she took Lori's necklace. Emily tells Jessi that tomorrow brings a clean slate and she can start over and make amends (not knowing why Jessi is so upset). Kyle gets a vision from Stephen's comatose father, and Amanda urges him to try to communicate with Stephen's father, as she believes Kyle is supposed to help Stephen and his father reconcile after years of not talking with each other. Kyle draws the things which he sees (a room which is the room Stephen's father lived in and a church). Stephen tells Kyle that the reason he was estranged from his father was due to his lack of faith in religion while his father was deeply religious. Stephen had written a note to his father when the kids were born and hand delivered it to his dad, but without even reading the letter he tears it up in front of Stephen. The letter had told his father that he would like him back in his life with the kids. Kyle keep seeing the numbers 15 11. He writes down all the possible things which it can mean but to Stephen it means one thing Luke 15:11, his father's favorite part in the Bible. Picking up the bible which he took form his dads house he sees the letter taped back together bookmarking the page. Stephen was able to let go, knowing his father really did care about his life and the choices he made after fearing that he might not have. Emily takes Jessi into her office to get "reprogrammed" so as to not act so much like a teenager, having been forced to in order to keep her daughter safe from Madacorp. Lori gets her necklace back after finding it in her locker, freaking her out as no one but the audience knows that Jessi was the one who stole it after attacking her. The episode ends with Amanda and Kyle kissing for the first time in a garden where Amanda used to go with her father before he died.

When Kyle discovers Foss unpacking the training materials in the warehouse, he interrogates Foss about his recent disappearance. Kyle reveals Baylin's message ("Don't trust Foss") to Foss, who denies any wrongdoing. Back at home, Kyle and Declan are distressed when Lori announces her intention to visit the site of a recently-murdered camper (which just happens to be the former location of Zzyzx). Declan theorizes that Lori is trying to prove that she has recovered from the attack; he and Kyle unsuccessfully attempt to dissuade Lori from her plan. Jessi, fresh from re-programming, arrives at the house and proceeds to ignore Declan and focus on Kyle. Amanda is initially reluctant to join her friends on the excursion; however, she changes her mind when Jessi invites herself on the excursion. Josh has realized that he has feelings for Andi, and tries to enlist Kyle's assistance in analyzing her moods and body chemistry while they tag along as well.

In the woods, a drunk Lori quickly stumbles upon an underground entrance to Zzyzx and disappears inside. Kyle and Declan follow her with concern, leaving Jessi, Amanda, Andi, and Josh outside. Jessi later sets out to look for Kyle, followed closely by a jealous Amanda. As Kyle and Declan look for Lori, Kyle starts experiencing strange visions of the Zzyzx from the past. Through his visions, the events leading to Kern's betrayal of Baylin play out in front of him. Baylin, horrified by Kern's intention to leave Kyle in the pod indefinitely, demands that Kern recognize Kyle's humanity, to no avail. Baylin's partner, Taylor, tried to make Baylin understand that the experiment is important to science, and that he should not let his emotions cloud the goal. Baylin, disturbed, flees to his secret safe, but is prevented from opening it to recover its contents. Kyle also watches Tom Foss watching over him in the pod, and playing classical music for him. As he watches, he observes the increasing panic among the scientists as it became obvious that the unconscious Kyle was rejecting their programming (i.e. making judgment calls, refusing to process strategic war scenarios). He watches in horror as the scientists methodically disconnect his life support mechanisms, but knows that Foss will somehow save him. Meanwhile, Jessi interrogates Amanda, trying to discover the root of Kyle's feelings for Amanda. When each girl declares her claim to Kyle, Jessi's emotions trigger a tremor that opens up a methane gas leak. Jessi begins having flashbacks to her birth, in the flames of the fire-bombed Zzyzx; the strange memories and visions upset her further, and she runs off alone. Kyle and Declan find Amanda and Lori. Kyle, realizing that he has the entire mainframe of Zzyzx downloaded in his head, quickly identifies an exit route for his friends, and sends them to safety while he searches for Jessi.

Meanwhile Josh admits his feelings to Andi, who simultaneously reveals that she has cancer. They are interrupted by Lori's cries, and they run to help. Kyle soon emerges from the drain pipe carrying Jessi, but runs back in to recover the contents of Baylin's safe (a box). Struggling for air, Kyle emerges from the exit right before he collapses. As Amanda revives him in present day, he flashes back to his earlier death at Zzyzx, and remembers Foss saving his life. When he regains consciousness, he and Amanda kiss passionately. Jessi watches with sadness and resignation.

At the Rack, Andi refuses to talk about the cancer and requests that Josh keep it a secret. Kyle checks on Jessi, who thanks him for saving her life and notes that he helped her not feel alone. Kyle returns to Amanda, disappointed that he had been unable to retrieve the box from the safe. Amanda surprises him by pulling the box out of her purse. Kyle returns to the warehouse, where he finds Foss striving to discover how the message from Baylin had been tampered with. Kyle tells Foss that he trusts him, and that he knows that Foss saved his life. As Kyle wonders who would have wanted to destabalize his relationship with Foss, he recalls surveillance footage from the mainframe of Zzyzx revealing that Taylor had been the one to betray Baylin.

The key to opening a box Kyle found in the ruins of Zzyzx depends on him gaining entry to Madacorp and getting his hands on Ballantine's ring, which was originally Baylin's and given to Kyle by Taylor. The Tragers are having a family dinner night and Kyle invites Amanda as a date, she wears the same thing she was wearing when Kyle first saw her playing the piano. Stephen's boss, Mr Ballantine unexpectedly shows up with Stephen. Everything seems fine until Kyle notices the ring on his finger, it's the one he sold to the pawn shop, he knows he must get it back in order to open the box Adam Baylin left behind. Kyle goes with Stephen to work pretending to need some research for a school project but really wanted to see the type of security Madacorp has and how he can get his ring back. He discovers that Mr Ballantine only removes his ring when viewing Madacorps newest project CIR (cerebral impulse relay) as it works like a giant magnet so all metal must be removed from their pockets etc. Kyle knows that he must get the ring then, when Ballantine is viewing CIR the following day to do a systems check.

Lori and Nicole show some signs of suspicion over Stephen's business to San Francisco with Emily. He seems to act different when talking to her etc. but he says it's innocent and it's easy to talk to her etc. Of course Emily is purposefully trying to plant seeds of doubt in the Trager family and make it appear as if Stephen and her are having an affair. After getting a call from the hotel in San Francisco saying a pair of contacts were left behind (Stephen doesn't wear contacts but Emily was wearing glasses when she dropped Jessi off for her appointment with Nicole and said she lost hers). Lori goes to confront her father at his office and that is when she disrupts Foss's plan to get the ring. Stephen assures Lori that he is not having an affair but the damage is still done.

Josh and Andi are still having trouble but that is only because Andi doesn't want to talk about her having cancer and Josh does. He wants to get closer to her because he likes her so much. He talks to Nicole about it, as a patient and learns that he needs to show Andi that he will be there for her through his actions rather than talking about it. Andi later tells Josh that tests showed that she will have to have treatment and so Josh lovingly gives her a Popsicle as it's supposed to help keep her hydrated during treatments. Andi is obviously happy to know that Josh isn't freaking out but rather willing to be with her through the treatments. Amanda and Kyle plan to go to a concert together as Kyle wants to spend more time with her. Amanda is nervous about what to wear around him because he remembers ever little thing so she consults Lori. She also tells Lori that she got accepted to a music/arts school in New York and isn't sure if she wants to go because of having to have a long distance relationship with Kyle for a semester.

During her session with Nicole, Jessi draws some pictures and Nicole notices that it is in the same way Kyle draws things (Pointilism). She asks if anyone showed her to draw like that and Jessi says no but wonders if she is doing it wrong. Nicole is starting to figure out that there are some similarities between Kyle and Jessi. She later studies one of the pictures and sees the Zzyzx symbol that Jessi drew (when she was escaping Zzyzx as it burned) and notices it is the exact same one Kyle drew. Later Jessi discovers Emily's safe containing a photo of her daughter Paige and other information about her life that she is keeping from Jessi. Jessi then goes to the park where Paige is attending a birthday party and talks with Paige, and says she's just a friend after drawing her a lion (in Pointilism). Emily picks Paige up and sees the picture and gets frightened she knows Jessi must have been there (as Paige drew a picture of herself with her 'friend' who was Jessi, and Emily knows Jessi draws in that dotting pattern).

With the help of Foss and Declan, Kyle plans to get back into Madacorp when they are doing a company wide system check of sorts. They manage to make a distraction and do an almost james bond type of planning to get the ring but their plan is foiled when Lori shows up to see her father, just before Foss can get the ring. Kyle and Declan manage to escape Madacorp with the ring though Foss gets caught after giving the two time to escape.

Ballantine meets Taylor at the Madacorp office, and we learn that Ballantine does not know the significance of the Latnok ring (ring Kyle took back). Taylor is seen wearing a similar ring, another Latnok ring indicating that he is part of the Latnok society. Ballantine said that 'his' ring was an heirloom passed down from his father, however it is unknown if this is true or if he was lying.

Kyle finally opens the box Adam left only to discover a photograph of what appears to be himself (a younger Adam) with a strange younger woman who looks exactly like Jessi. On the back of the photograph is written in Hunngarian "A fény majd megmutatja az utat" meaning that "the light will show the way". Due to Kyle's periodic absences, Amanda questions their relationship, but the two share a kiss and all seems to be forgiven for now. Though Kyle is anxious to talk with Jessi to find out what other connections they might share.

After finding a photo of Adam and a Jessi look-a-like locked in Baylin’s box, Kyle and Declan realize that the best way to crack the mystery of Jessi is to get close to her at the high school charity event. The event is to raise money for cancer patients, which 'hits a nerve' so to speak with Josh who is still trying to deal with Andy having cancer. Josh decides that he wants to try and win the hybrid (a Toyota Prius) for Andy to show how much he cares for her. However, Josh isn't one of the lucky ones who win the raffle and are given a chance to win the car. Though that doesn't stop him, he buys a winning ticket off a guy so he can join Kyle, Jessi and the other contestants who will be vying for the car. Kyle realizes that this is the perfect opportunity for him to talk with Jessi and figure out more about her. After predicting to Josh that a few contestants will dropout from the competition he is able to talk one-on-one with Jessi. He tells her that he wants to help her etc and gets her to reveal a little about her self. They have a few moment throughout the episode talking and such. At this time Lori calls Amanda and tells her that she needs to get down to the event and support Kyle to show Jessi that she can't have him, Lori is obviously still bitter towards Jessi.

With Lori's encouragement Amanda goes to the contest to bring Kyle a survival kit of sorts as well as offer her support, though in reality she wants to keep an eye on him as well as look her best to. Hilary is creating an audition tape for a reality show and so she is acting as a journalist. Though really she is just trying to find dirty secrets about the contestants. Though Lori is supporting her search, especially towards finding info about Jessi. Hilary ends up reviewing video taken from the dance where Lori was attacked. It is revealed that Jessi has Lori's necklace at the end of the evening, letting her and later Declan and Lori know that Jessi was the one who attacked and then stole the necklace. Lori is angered and promises to punish Jessi. Hilary also finds footage of Josh buying a ticket from the contestant he replaced and ends up revealing to Andy that Josh cheated to get into the contest to win the car.

Andy confronts Josh about how he got into the contest and she ends up revealing to everyone that she is the girl with cancer as the two are fighting. Josh ends up running after her, disqualifying himself from the contest, leaving only Jessi and Kyle left. As Kyle talks to Jessi again they touch hands and he is able to see into her mind. They both filter through her memories, the ones that Madacorp tried to make her forget/erase as they reveal that she is not a normal girl or sister of Emily. As Kyle sees Jessi's memory of being found and shot by Emily a large blast occurs and Kyle and Jessi fly into the air. Both are alone, after being checked by a metic, in a tent on cots. Kyle now knows who Jessi is after seeing her memories however Jessi doesn't realize how alike the two are. Kyle and Jessi both reveal to one another that they don't have a bellybutton, just as Amanda walks in to discover that Jessi is touching Kyle's stomach while holding her own shirt up. Amanda not understanding the reality of the situation believes that Kyle is cheating on her, so she storms out. Hilary decides quits as a reality star/journalist as it destroys too much.

During the contest Emily and Stephen are at Madacorp running trial tests on the CIR. Stephen is unaware that the test subject is Tom Foss. Lori still questions her father's fidelity which becomes very apparent when Emily and Stephen arrive to the contest to check on Kyle and Jessi's status. Lori tells Emily to keep her 'psycho sister away from her family' but finds no support from her father. Kyle tries to explain everything to Amanda who tells him that Charlie said the same things and that she wants to know if he questions their relationship. Andy and Josh talk and he explains his actions and the two makeup. They then share a passionate kiss after Andy decides to finally "go public" (though she already did when she yelled it out at the contest) about her having cancer by making a tshirt that says "cancer girl" as well as providing Josh a shirt that says "I'm with cancer girl".

Emily arrives home after searching for Jessi, who disappeared from the contest after realizing that Emily was not her sister and that she shares a lot with Kyle. Emily finds Jessi at home but is surprised to also find her daughter Paige there. Jessi demands to be told the truth about everything, and she wields a knife to prove to Emily that she doesn't want to hear lies. At the end of the episode it is revealed that the police went to find Jessi to question her about the whole Lori incident however it is revealed that Jessi has run away.

Jessi is out of control causing tension within the Tragers' home. After recent events, all members of the Trager family are on lockdown until Jessi is found. Lori enlists the help of Hillary to plot her revenge on Jessi. Though Hillary then turns into therapist to help Lori and Declan solve their issues as a couple. Josh plans a fun day of junk food and video games with Andy, but as it begins, she mentions that it will be their last day together. Josh asks why and she tells him that it is because she starts chemo tomorrow. Andy doesn't want him to see her puke and suffer and sympathize for her so she tells him that they should make their last day together special starting with a make out session. Josh doesn't enjoy it much because the fact that he won't be able to see her anymore ruins it. Later Andy makes peace with him and tells him that they can still continue to see each other. Things explode between Stephen and Nicole when she confronts him about his “affair” with Emily. Meanwhile, Kyle struggles to figure out how he should deal with Jessi. Upset that he is the reason for all of the Tragers’ issues he looks for a solution to fix everything.

Andy and Josh end up getting in another confrontation as Josh is tired of hearing that this will be his last day with Andy. He tells her that he wants to be able to see her everyday, even if she is going through treatment. Andy tells him that she wants to protect him and keep him from having to go through all that pain seeing her. However, she later concedes and tells Josh that they can stay together and see each other while she is going through chemo. Lori tries to take out some aggression by throwing darts at a headshot of Jessi, though after sitting through counseling with Hillary she realizes that there isn't a point to it all and that holding a grudge isn't important in life. Lori and Declan share a moment and it appears that the two have made a step towards rebuilding their relationship.

Kyle falls asleep in his tub and has a "talk" with Adam Baylin, which turns out to be his conscious. Kyle tries to figure out if he should go after Jessi or not. He receives a mysterious call from Emily who encourages him to find Jessi since she told her everything. It is also revealed that Emily warned Stephen to go home and that she feels Kyle's family, the Trager's could be in danger. This compels Kyle even more to leave since all those whom he loves have been put at risk because of him just being there. Finally during his conversation with Adam/himself he comes face to face with Jessi. Adam tells her he should talk to her to figure out where the real Jessi would've gone. Kyle and Jessi discuss whether or not she is even worth saving. Ultimately Kyle decides that he must find her in order to save both Jessi and protect the Tragers. Jessi ends up finding Jessi in the woods where she had confronted the hunter who attacked her, the same one which she ended up killing. He coaxes her away from the edge of a ledge where she is contemplating suicide as she wants to "make it all stop" she is obviously troubled and having a difficult time dealing with the fact that everything she thought was real was just a lie and that Madacorp wants her to betray Kyle. Kyle tells her that they will go together on a "mission" to find out the truth about their past and that they wont return home until everything is over. Kyle is determined to fix everything and have a normal life again, one in which his family and friends and now Jessi aren't threatened by Madacorp. Jessi agrees to go and the two set out to find out who they are and where they came from.

Kyle decides that he and Jessi cannot return until the conflict with MADACORP is resolved. Emily releases Foss claiming that she feels guilty for invading the Trager's lives, and for manipulating Jessi. Foss then calls Kyle and tells him to go somewhere, that Kyle "has everything he needs". Ballantine berates Emily for releasing Foss, but she claims she thought he would lead them straight to Kyle and Jessi.

Kyle finds a small pinhole in the back of Baylin's ring that displays a map when light is shone through it. He and Jessi follow the map and find the diner where the picture of Baylin and the mystery girl was taken. Kyle notices that their is a postcard stand with the exact same postcard that he sent to himself in a previous episode, he also notices a fish bowl with goldfish in it. Kyle clearly has feelings that he might have been their before or that he knows that their is some special connection to his and Jessi's past. The owner is old and senile, according to his daughter, but he clearly remembers Baylin and the girl. He says that they were in love and such a happy couple and that they would always play the song "She Could Be You" on the jukebox, that it was their song. Kyle and Jessi try to play the song but notice that the cd is missing. They decide to sit at a table and figure out how to get to route 12. They discover from the owners daughter that the route had been washed out years ago and that they should be careful up there. Jessi contemplates leaving because she is afraid she will betray Kyle after seeing into Kyle's mind when he has a daydream of kissing Amanda. The two realize that they can see into each others minds without touching. Kyle convinces her to stay and that he trusts her after he notices "A & S Forever. '82" carved into the table they are seated at. He knows that the A is for Adam and that the S must stand for the mystery girl in the photo (there is also the Latnok/Zzyx symbol carved on the table). Kyle explains that it is all apart of their history and that the two of them must work together to discover the truth.

Meanwhile, Foss is watching/listening to the Trager's on Kyle's orders to protect his family. He and Declan try to make sure that Kyle's secrets are kept though Declan knows that it is only a matter of time before they figure things out. The Tragers are pooling all of their evidence about Kyle and all the strange occurrences connected with him, trying to decide who or what he is. Josh strongly maintains that Kyle is he and Lori's brother, and Nicole and Stephen's son and leaves. The Tragers call Declan to come over so he can explain what he knows about Kyle. When he refuses, Stephen decides to call the police, but is stopped by Foss, who had been watching them per Kyle's request. Foss tells the Tragers that he has known Kyle since he was a child and that Kyle has had a hard life. Stephen tells Foss that he can take care of his own family, and to leave. The Tragers decide that no matter what, Kyle is family, and he can explain about himself. Stephen and Nicole realize that Josh is right and that Kyle is their son and so they tell Foss to go find their son.

After leaving the diner, Kyle and Jessi find Route 12, which has been washed out, but they continue on foot, eventually coming to a seemingly abandoned log cabin. In the basement, they find a door with the Latnok/Zzyx symbol on it. It has a lock that resembles a piano keyboard. Kyle realizes that the code must be the song they were told about at the diner. Kyle calls Amanda who looks up the song and plays it for them. Behind the door they find Adam Baylin in a coma hooked to an EKG. Kyle decides he can communicate with him, but fails after several tries. He asks Jessi to help and she reluctantly agrees. As they open their minds to each other to speak with Baylin, Baylin tells Kyle that Jessi has betrayed him and for him to stop. She has taken the Zzyzx information from inside his head, and out of fear runs away. When Kyle catches up to Jessi at a cliffside, Kyle asks why she took the information, and she claims she could not help herself. They fight, and Jessi tells Kyle that he never should have trusted her and jumps over the cliff, to Kyle's shock. The episode ends in a cliffhanger of sorts leading us to question the fate of Jessi.

NOTE: The second half of season 2 will conclude early 2008 with 10 episodes.

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