Some time later, Kyle was deep into training his powers with Adam Baylin while trying to stay in contact with the Tragers, something Tom Foss was against because he feared Zzyzx would track it. After leaving a web cam call on too long while Adam Baylin collapsed, Zzyzx was able to track the call and apparently assassinated Adam.
In retaliation, Tom Foss firebombed the Zzyzx complex while Kyle tried to stop him. Kyle wanted to go back to the Tragers and was taken there by Adam's long time friend Bryan Taylor. Brian masqueraded as the Peterson's lawyer and told the Tragers that they had died in a car accident.
Later in the woods near the Zzyzx site, a girl is seen walking around, naked and covered in a strange pink "goo". She wonders to a camp site and began to pick at the food over the fire. A tall male camper/hunter turns around and surprised to see a naked girl standing there. He approaches her and touches her arm. The girl, Experiment 781228, is threatened and protects herself by grabbing the man's throat until his lifeless body drops to the ground. She takes his clothes and runs. Julian Ballantine then hires a woman by the name of Emily Hollander to find 781228 and return her to Madacorp. Madacorp then "programs" 781228 to believe she is Emily's little sister Jessi Hollander. Upon Kyle's returned to the Trager family he is shut out by Declan because he refused to tell him what had happened while he was away. Kyle was upset to hear that Amanda was still dating Charlie.
Later, Kyle continued to train with Tom Foss while simultaneously trying to tell Amanda the truth about Charlie. In the end, Amanda learned about Charlie's cheating during a school poll and got angry with Kyle for not telling her sooner. Kyle tried to get on Amanda's good side while still training with Foss. The training began to take it's toll on Kyle's relationships. Amanda wouldn't listen, but eventually calmed down and asked for time from Kyle. During this time someone broke into Amanda's home and apparently stole a personal item.
In order to become friends again, Kyle decided to track down the man who broke into the Bloom house to retrieve Amanda's stolen necklace, only to find that Carol Bloom had pawned it. Kyle sold the Latnok Society ring to get it back, which apparently was then purchased by Ballantine.
Kyle and Amanda decided to go to the Lori and Andy Jensen's alterni-dance, but Kyle was dismayed to hear that Amanda's mother grounded her for their activities that morning. Kyle went to the dance and was happy to see Amanda had snuck out. Lori has attempted to befriend a new patient of Nicole's, Jessi Hollander by inviting her to the dance. At the dance Kyle and Amanda dance together and were about to kiss just asJessi blew out the lights when her sister, Emily attempts to drag her away from the dance. Amanda then kisses him on the cheek and says that she would like to go out another time.
After the dance, while cleaning, Lori is attacked outside and her necklace, a gift from Declan is stolen. Kyle later helped Stephen try to connect with his comatose father William Trager. After hours of trying, Kyle finally managed to "talk" to William and managed to tell Stephen that William did read the letter that he thought William had ripped up and forgotten about. Kyle and Amanda later meet in the park, where they have their kiss.
Kyle refused to believe anything the newly returned Tom Foss told him because of a recorded message he had received from Baylin. Kyle also refused to continue training with him. Kyle reluctantly joined Lori and the other kids to the camping site where the camper was killed, only to discover the ruins of Zzyzx. He had flashbacks which seemed like old home movie reels, of his early life and Kern's betrayal, only to discover that it was Brian Taylor and not Tom Foss that had also betrayed Adam Baylin. Jessi also began to have flashbacks of her violent past. Not knowing what they were she gets scared and can't make sense of it all.
Sometime later, Stephen invites his boss Julian Ballantine for dinner. Kyle quickly noticed the Latnok ring on his finger, believing it to be Adam's. He conspired with Tom and Declan to sneak into Madacorp and steal the ring back. He managed to take it off of Ballantine's hand right before escaping down a stairwell, but Tom was captured in the process.
Kyle received a fake call from Tom saying he was okay, so he felt okay in going to the charity event and competing in the Hands on a Hybrid competition. He took the opportunity to get to know Jessi, managing to read her memories when they held hands, eventually causing the lights to crash. Later, Kyle showed Jessi he did not have a bellybutton. Jessi touched it just as Amanda came in. Kyle tried to defend himself, but Amanda said he was acting just like Charlie.
The Trager kids tried to leave the home but Nicole told them that they were on Lockdown because of Jessi. Kyle paced back and forth with Josh trying to come up with an answer about Jessi and when Amanda came to visit, she told him about her schooling. He told her that whatever she decided, he would always be there. Later on, Kyle listened to everyone arguing and suddenly, the noise stopped. He looked up, and there was Adam Baylin. It was revealed to be Kyle's consciousnesses, and after Emily Hollander called Kyle to look for Jessi, he saw her also. Kyle left the the Trager's to go find Jessi near Zzyzx, but not before being confronted by Nicole. Nicole wondered what connection Jessi and Kyle said, but he said to trust him and that it was all for them. Kyle left and stopped Jessi from jumping off a ledge, and he told her that they were not going back until it was over.
Kyle and Jessi find a hole in the Latnok ring, and after showing Jessi the picture of Adam and S., they use the car lights to see what is in the ring: a map. It led them to the diner that Adam and his mysterious love with the first initial of S would go to eat. An old man claimed that he had seen them in there a while back, (25 years to be exact) but his granddaughter explained that he just thought they looked familiar. Kyle and Jessi got a table that had A+S June 1982 written on it. (Assumed to be Adam Baylin and S) Kyle and Jessi then decide to go to the end of Route 12 , where they find a log cabin. Inside the cabin, there was not much until they found a secret passage to the basement. Inside the basement, there is another door that required a musical code to get in. Kyle guessed that the code was the tune to D4, the code on the back of the photograph of Adam and "S" and the missing 45rpm record at the diner. The tune "She Could Be You".
Kyle then calls Amanda and asks her to find the song and play it for him. While Amanda plays the song Kyle gets lost in her music. He missed Amanda and wishes he could be there before she leaves for her music program. After Kyle and Jessi enter the code then enter a room illuminated in blue light and the sounds of ventulaters. There on a bed, being kept alive by ventulaters, a failing body, was Adam Baylin. Kyle figured that the ashes he scattered were not Baylin's, and he and Jessi attempted to communicate with Adam. Adam told Kyle not to trust Jessi, "she's betrayed you". She disconnects from them and runs out of the cabin and to the water falls. She says she did what Mada Corp told her to do for her freedom and after a physical fight against Kyle she tells Kyle that he shouldn't have trusted her. With that, Jessi jumped off the ledge into the waterfall.
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