Son of Man – Season 1 ends with Stephen trying to stop the Machine and the extermination of humanity, but he fears he may be too late. Meanwhile, Russell realizes that his alliance with the Founder is a mistake and tries to rescue Cara; and Jedikiah offers John an intriguing opportunity that could lead to them working together again.
Kill Switch – Russell decides to sacrifice Roger. Meanwhile, John turns to Astrid for advice.
A Sort of Homecoming – Everyone becomes concerned about the consequences if the Founder learns that Roger may return. Meanwhile, Stephen tries to destroy the machine the Founder has been using to train him; and Russell loses hope that the Refuge will ever be found and chooses to head out on his own with some other Tomorrow People.
Modus Vivendi – Stephen eyes a potential truce between the Tomorrow People and Ultra, but Cara sends Russell to meet with the Founder. Meanwhile, Jedikiah goes on the run and tries to keep Ultra from discovering his secret; and Stephen tries to contact his dad once again.
Smoke and Mirrors – Stephen tires of Jedikiah’s constant lies about his father, so he makes a choice about his alliances, and he tries to bring in a new break-out to Ultra to see if things have really changed. Meanwhile, Stephen’s brother disappears after Jedikiah forces Stephen to protect him.
Endgame – 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. Madeleine Mantock also stars.
Superhero – The Tomorrow People and Ultra both try to recruit a new break-out who is doing good deeds. Meanwhile, Morgan betrays Jedikiah’s trust to help the Tomorrow People; and Jedikiah discovers some surprising information.
Enemy of My Enemy – Julian is caught by Ultra and forced to strike a deal that could cost his and Stephen’s lives. Meanwhile, Astrid is haunted by nightmares after her near-death experience and turns to her new friend John for comfort.
Brother’s Keeper – Stephen gets some shocking news and tries to restore order in both of his worlds by making a deal with Jedikiah. Meanwhile, Cara and Russell attempt to lure in a new break-out; and Jedikiah gets closer to developing a secret technology that could change his future.
Things Fall Apart – Stephen gets upset with Jedikiah for going back on his word, leaving Stephen to face the Founder. Meanwhile, John and Cara clash, forcing Cara to issue a harsh punishment; and Stephen learns a surprising secret about his mother.