Kyle XY: a story about a 16 year old boy with a mind of a genius. He's found wandering in the streets with no memory of who he is, or where he comes from. He's soon taken to a youth detention center, where he meets Nicole Trager, a psychologist. She sees that Kyle has these amazing abilities. It's not long before she wants to bring him home to her husband and two kids. Stephen at first has his doubts about Kyle. While staying with the Tragers, Kyle starts to remember and is willing to go all the way to unlock his past.
Restrained and weakened, Kyle awakens inside a Latnok building. Despite his predicament, Kyle must escape and rescue Amanda—who is being held in the same building.
Kyle fears for Amanda's life after a psychic gives him a stark warning.
Jessie begins to settle into the Trager's house. Meanwhile Kyle tries to figure out what Latnok did to Amanda with the help of Jessie, which ultimately leads to some unwanted conflict with Kyle and Amanda's relationship.
Kyle hits the bar with Josh and Declan to drown his sorrows after breaking up with Amanda. Lori and Jessi bond over boys as Lori uses Jessi's apartment as a bolthole.
A car accident seriously injures Nicole, and Kyle and Josh help a woman named Gretchen give birth.
After Cassidy helps to save Nicole’s life, Kyle is a man of his word and begins to pay his debt back to Latnok. But what Kyle finds is a complete surprise -- Latnok is not some dark scary place…but rather a hip college hang-out for young and bright minds, including Mark. Still not willing to give them the benefit of the doubt, Kyle decides after his first day there never to return, but rethinks his decision when he finds out about his family’s financial dilemma. Will Kyle sell his soul to the devil to help out the Tragers, or can he find another way to get a hold of some quick cash? Meanwhile, Jessi comes clean about everything to Kyle, which brings about mixed results.
Kyle deals with Jessi's announcement and jealousy over Nate, and Josh reels from Andy's news. Meanwhile, Kyle – still suspicous of Cassidy – makes a plan to expose him.
What Jessi and Kyle find in Cassidy's safe sends them searching for the truth about Sarah Emerson, but Jessi's unrelenting method may endanger her life. At home, Declan finally puts his foot down, and Josh already misses Andy.
Kyle risks losing Cassidy's trust when he begins a deception aimed at discovering Latnok's true purpose, and Jessi, devastated by their discovery, has a hard time putting aside her emotions. Elsewhere, Josh plans a perfect farewell for Andy.
With Adam Baylin's help, Kyle begins to realize the truth behind his existence but soon finds himself back at the Trager's house under the training of Tom Foss.
Kyle wonders if he made the right decision about returning to the Trager household, especially when he realizes how much he can't tell them. Meanwhile, life outside of Zzyzx begins for XX.
Kyle's attempts 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.
Foss is alarmed by a murder in the forest, which pushes Kyle to his breaking point. Declan's probe of what he believes in Kyle's secret could have major consequences.
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. Meanwhile, Kyle's on a mission to find Amanda's stolen bracelet.
Kyle believes he can predict the future after having multiple visions, which all come true. Hedelves deeper into Baylin's research hoping to find an answer.
As Kyle and Amanda prepare for their first date, a cryptic warning about Tom Foss makes Kyle wonder whom he can trust. Meanwhile, Jessi chafes at Emily's restrictions.
Kyle's visions offer the Tragers solace after Stephen's father suffers a stroke and falls into a coma. Meanwhile, Jessi's lack of progress at therapy dismays Emily.
Lori, Kyle, Jessi, Declan and Amanda stumble upon the ruins of Zzyzx while on a camping trip in the woods. Andy shares a life-changing secret with Josh.
Kyle, Declan and Foss plot to retrieve Kyle's Latnok ring. Meanwhile, Lori begins to question Stephen's time at Madacorp.
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.
An out-of-control and missing Jessi increases tensions within the Trager household, forcing Nicole to institute precautionary measures.
Kyle breaks quarantine to find Jessi and they use the photo from Baylin's lock box to search for answers. Meanwhile, the Trager's sort through all that they know about Kyle in order to make sense of who he really is.
Believing Jessi is dead, Kyle returns to the Tragers and reveals the truth about Madacorp. He's now determined to take down MadaCorp and destroy all the information they have on Zzyzx.
It's Career Week at school. As Kyle and Josh contemplate their respective futures, Jessi's quest for acceptance clashes with Kyle's need for anonymity. Meanwhile, Brian Taylor seeks parenting advice from Nicole.
Kyle and Amanda's relationship hits a period of uncertainty after she makes a surprise visit home, but is uncharacteristically cagey about the reason why. Meanwhile, Jesse loses her patience with Kyle when he keeps putting off her training sessions.
Amanda's presence puts the Tragers into an awkward position when a social worker comes to evaluate their fitness to take care of Kyle.
Amanda gets a job at The Rack, but her first day does not go well. Meanwhile, Jessi's presence in Kyle's life continues to irk Amanda, and Josh is placed in a difficult situation when $120 goes missing from The Rack's cash register.
Hoping to work things out with Jessi, Kyle takes her on a trip to research Sarah. Meanwhile, Lori and Hillary con Amanda into visiting a college bar in search of a DJ, and Andy and Josh seek couples counseling.
Kyle begins having cognitive malfunctions and is drawing pictures in his sleep due to the attention demands from the other students during his midterm exams. Meanwhile, Kyle's condition has Jessi creating her own tutoring service.
Kyle and Josh become involved in a complicated cheating scandal at school. Meanwhile, Jessi is being pushed by Taylor to train for the Latnok presentation.
Sarah asks Kyle to intervene with Jessi, but his method may prove disastrous; Brian Taylor hits a wall in his quest for Latnok's approval, and the prom has a serious cash-flow problem.
The teens scramble to make their prom night as perfect as possible, and Jessi makes a surprise announcement regarding her relationship with Sarah.
A teenager is found disoriented in the middle of traffic and taken to a detention facility. Later, Nicole Trager, a psychologist, comes to examine him, and takes him home. He gets on the bad side of both Trager kids, Josh and Lori, and annoys Stephen, Nicole's husband. But one by one, Kyle influences them to accept him.
Kyle encounters the concept of time and wonders why those around him focus on it. In an attempt to tire out Kyle, his family subjects him to running, sleeping pills and other activities. Josh suspects that Kyle may be an alien.
Nicole has things to attend to, so other members of the family have to babysit Kyle, who's having trouble processing the little white lies that his family tell. Meanwhile, Steven learns that he'll have to lay off employees & Amanda freaks out over a fender bender.
Kyle attempts to figure his emotions and sudden attraction to next door neighbor Amanda, while Lori and Josh are also experiencing love pains of their own.
Kyle, Lori and Josh experience difficulties on the first day of school while Nicole and Stephen receive a visit from Tom Foss.
Kyle becomes frustrated when he experiences his first brief flashes of memory, and he ultimately finds comfort from Amanda. It's the day of Lori's birthday, but she's not excited about it while Kyle on the other hand, wishes he even knew the date of his birthday.
Kyle links his memory to a missing professor, but finds a welcome distraction when he joins the basketball team. Meanwhile, Nicole gains a better understanding of Kyle's unique situation.
After an unusual hypnosis session, Kyle is determined to unlock his memory, so he accompanies Lori and Declan to the University of Washington to search for clues about the missing Professor Kern and how his relationship ties in with Kyle.
Kyle discovers that he has the ability to read lips and listen to distant conversations, so he recruits Declan and uses the newfound abilities to investigate Tom Foss. Meanwhile, Josh stresses over his grades. Amanda's boyfriend has a terrible secret.
The Petersons, Kyle's real parents, arrive to take him home, but Kyle is skeptical about his biological ties, so he turns to Tom Foss for answers. Meanwhile, Steven has trouble accepting that Kyle may be leaving.