After Stephen breaks Ultra protocol during a training exercise, Jedikiah’s mysterious boss insists on meeting Stephen. Stephen grows concerned when he learns Jedikiah is unable to protect him, so he turns to John, who is only interested for selfish reasons. Elsewhere, the Tomorrow People are desperate to go topside to a party like normal people, but John and Cara disagree on the dangerous plan. Meanwhile, Stephen makes a plan to go to Homecoming with Astrid, but when he bails on her once again, she decides to find out what he is really up too.

Stephen is determined to uncover what he hopes is the key to finding his father, and crafts a plan with the Tomorrow People that involves getting inside Jedikiah's head. Meanwhile, Cara and Russell encounter an uninvited visitor in the subway tunnel base. Stephen takes a risky opportunity and snoops around Ultra.

When John finds himself in a dangerous situation, Stephen is unable to help without revealing himself to Ultra. Not satisfied with the answer he has discovered about his father's disappearance, Stephen decides to take drastic measures with the help of his fellow Tomorrow People to find out the truth. Meanwhile, Cara and Russell negotiate a trade with Jedikiah, which ultimately makes Jedikiah take a big risk.

Stephen is upset with Jedikiah for going back on his word, leaving Stephen to face The Founder. In order to protect Astrid, Stephen has to make a dangerous deal to bring in a powerful break-out. John and Cara clash, forcing Cara to issue a harsh and unexpected punishment. Meanwhile, Stephen learns a surprising secret about his mom.

Stephen stumbles upon a clue that the Tomorrow People have been desperately searching for. John and Russell learn of a dangerous plan that Jedikiah has in the works, but no one could have predicted the ultimate outcome. Meanwhile, Cara gets a lead on a new break-out, but is shocked to discover that it’s someone from her past.

Fed up with Jedikiah’s constant lies about his father, Stephen makes a choice about his alliances. Trusting in Ultra and Hillary, Stephen wants to bring in a break-out to Ultra to see if things have really changed, much to Cara’s dismay. Meanwhile, Stephen’s brother goes missing after Jedikiah forces Stephen to protect him.

Stephen’s hard work as a double agent seems to be paying off with a potential truce between the Tomorrow People and Ultra. Still untrusting, Cara sends Russell to meet with The Founder. Jedikiah is now on the run and is desperate to keep Ultra from discovering his secret. Meanwhile, with the help of Hillary, Stephen tries to contact his dad once again.

With the possible return of Roger on the horizon, everyone is concerned about the consequences if The Founder were to find out. Stephen now knows the truth about the machine The Founder has been using him to train in and needs John and Cara’s help to destroy it. Meanwhile, Russell and other Tomorrow People have lost hope they will ever find The Refuge and choose to head out on their own.

When the Tomorrow People learn the truth about the serum they were injected with, Stephen and Cara attempt to buy time for Jedikiah while he tries to create a possible antidote. Growing impatient, Russell and the other rogue Tomorrow People make a rash decision to sacrifice Roger to Ultra for their own safety. Meanwhile, John is having a hard time figuring out his new role and the only one he can turn to for advice is Astrid.

Russell realizes his alliance with The Founder was a mistake, and tries to make up for his decision by saving Cara from an Ultra ambush. Stephen understands that he must be the one to stop The Machine and the extermination of humanity, but he fears he may be too late. Russell offers up a plan to help Stephen, but he is going to need everyone’s help, including John and Astrid, if they are going to have any chance to survive. Meanwhile, Jedikiah offers John an interesting opportunity that could have them working together again.