With Adam Baylin's help, Kyle begins to realize the truth behind his existence. He is homesick for the Tragers, and the Tragers miss him as well. After a security breach, Adam Baylin is shot and Kyle soon finds himself back at the Trager's house under the training of Tom Foss. As Kyle celebrates, a girl from a pod like Kyle's emerges.
Claiming that his parents were killed in a car crash, Kyle is back at the Tragers to stay. But his homecoming isn't as happy as he thought it would be as he must keep some secrets from the family he loves. Torn between wanting to be home and not wanting to keep anything from the Tragers, Kyle wonders if he should have come back after all. Meanwhile, XX begins her journey outside of the walls of Zzyzx.
Kyle finds that returning to his old life is virtually impossible, as Tom Foss hounds him to work on his new skills. Also, Kyle is devastated to know he played a part in Lori and Declan's break-up. Meanwhile, now that Ballantine knows of Kyle's existence, he has a new mission for Emily and XX to bring Kyle back at any cost.
After detecting a dangerous connection to the mysterious murder in the woods, Foss ramps up Kyle's training. Going along with his promise, Kyle sticks with it, even when it interferes with his "normal life." Meanwhile, Declan is on the hunt for what Kyle is hiding, but his quest takes a dark turn when Lori's life is threatened if he doesn't stop. Steven loses his job. Josh gets his license.
Nicole gets back into the swing of her job as she starts working with her new patient Jessi. Told by Jessi's sister Emily that she has had a rough childhood, Nicole thinks that she is just the person to help the lost teen.
Kyle starts to have premonitions that come true, which leads him to contemplate how much he knows about the future. He struggles to understand what is going on when he and Foss link the visions to possible Adam Baylin teachings. As Kyle digs deeper into Baylin's notes he gets an unexpected message from the past about the future. Meanwhile, the Trager family is also dealing with what the future may hold for all of them.
After receiving the warning about Foss, Kyle contemplates who he can really trust. He is at a crossroads and can't decide who to let into his life. Meanwhile, Jessi struggles to deal with Emily's strict restrictions on who she can and can't let into her life.
With Kyle’s help Stephen gets the opportunity to make amends with his estranged father when he has a stroke and is in a coma. Kyle begins to get visions that pertain to Stephen’s dad and Amanda pushes Kyle to help Stephen get the peace of mind he is looking for. Meanwhile, after a strained session with Nicole, Emily begins to realize that Jessi is not all that she is supposed to be.
Lori leads an expedition into the woods for an overnight camping trip that takes a dark turn. When Kyle, Jessi, Declan, Lori and Amanda get lost in the Zzyzx remains, the group struggles with their own demons as they try to find their way out. Meanwhile, Josh's attempt at wooing Andy goes sour when she drops a bomb that leaves him heartbroken and confused.
Kyle breaks into Madacorp to open up the mysterious box he got out of Zzyzx.
After finding a photo of himself and Jessi 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 is at the high school charity event. Once there, Kyle uses the opportunity to talk to the already vulnerable Jessi. Meanwhile, other secrets are revealed during the event as Lori finds out the identity of her attacker.
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. Josh plans a fun day of junk food and video games with Andy, only to be told that she can't see him anymore.
Kyle and Jessi go on a quest to find out the truth behind their connection, as well as their creation.
After his journey with Jessi ends, Kyle returns home and is ready to tell the Trager family the whole truth. With every sordid detail out on the table he wonders if they will be so willing to take him back. Once they hear everything the Tragers only support him more and rally around Kyle to take on Madacorp. With a plan in hand, the family heads to the company picnic to help Kyle take down the corporation’s secret machine.
Still shaken from her ordeal with Madacorp and the revelation of her father’s identity, Jessi struggles with who she is and what is in store for her. Looking for a clean start back at school, she wonders if using her super-human powers would be the key to the approval of the other students that she has been so desperately looking for.
After Amanda mysteriously returns at home from New York, she tells Kyle that they need to talk, but when he starts asking questions she rebuffs him and cuts off all communication. The Tragers try to cheer him up and tell him there must be a reason, but they all fear that the worst has happened. Meanwhile, Jessi becomes impatient with Kyle after he keeps postponing their training sessions to keep pursuing Amanda.
After receiving an anonymous complaint about Kyle, a social worker makes a surprise visit to the Trager home. What should be uneventful becomes tricky with Kyle harboring fugitive Amanda in his room and Lori hiding a closet full of beer. Plus, they haven’t figured out how to explain the reason for Kyle sleeping in a tub.
Suspecting Brian Taylor is using Jessi for darker purposes, Adam Baylin returns to entrust in Kyle a new assignment. Baylin wants Kyle to stay close to Jessi and be a positive force in her life. Unfortunately, Kyle finds that his new mission is easier said then done when he comes up against an upset Amanda, who doesn't understand their connection. Meanwhile, Josh deals with being left in charge at The Rack where things go horribly awry.
Feeling badly for neglecting Jessi, Kyle tries to make amends by taking her to the University of Washington to learn more about her mother, Sarah. As they follow a trail of information, Kyle starts to see Jessi's more aggressive and competitive side as well as how far her abilities have progressed.
With school midterms right around the corner and everyone demanding Kyle's attention, he soon feels like he is being pulled in every direction. When he starts experiencing brain glitches and produces weird drawings in his sleep, Kyle starts to wonder if it is more than just stress that is getting to him.
The grey lines between right and wrong are tested for several students when a school wide cheating scandal rocks the high school. After studying hard, Josh is devastated to learn that he is one of the accused while Kyle is shocked to find out he is suspected of being the ringleader. Josh and Kyle must clear their names and save the prom. Meanwhile, Taylor continues to push Jessi in her training for a Latnok presentation.
After Kyle is able to track Sarah down, she implores him to get Jessi away from Taylor. However, this task is easier said than done as Kyle must deal with Jessi's stubbornness and Sarah's adamant request to remain hidden.
After extensive research Kyle is still trying to figure out how to make prom night perfect for Amanda, but all of the teen movies in the world can't help him. Declan is also pulling out all the stops to show Lori how he really feels. Meanwhile, Andy hints at a special ending to prom, leading Josh to worry if he is ready to have sex. Jessi makes a surprising announcement about her future with Sarah.