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.
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.
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.
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.
Stephen stumbles upon a clue that the Tomorrow People have been desperately seeking; John and Russell learn about a dangerous plan that Jedikiah is plotting; Cara gets a lead on a new break-out but is shocked to discover that it is someone from her past.
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.
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.
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.
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.
Stephen feels uneasy about Hillary, a fellow trainee who has a secret agenda. Meanwhile, a family camping trip is planned by Stephen's mom that includes her new boyfriend. Stephen asks Cara and John to look after Astrid while he's away.
Stephen and his fellow Ultra trainees are given a test to see who is worthy of becoming an Ultra agent; Cara faces a mysterious visitor from her past; Russell is sent on a dangerous mission that could force a clash between Tomorrow People groups; John works with a new break-out.
The Tomorrow People try to free captives from Ultra's secret research lab. Meanwhile, Stephen believes he knows what happened to his father; and Stephen's mom introduces him and his brother to a new man she is dating.
John gets into a dangerous situation, but Stephen is unable to help without risking revealing himself to Ultra, and he decides to take drastic measures to find out the truth about his father's disappearance. Meanwhile, Cara and Russell negotiate a trade with Jedikiah.
Stephen devises a plan with the Tomorrow People to find his father by getting inside Jedikiah's mind. Meanwhile, Cara and Russell encounter an uninvited visitor in the subway tunnel base; and Stephen snoops around Ultra.
Stephen uses his newfound powers for fun, and Jedikiah takes extreme measures to make sure he doesn't do it again. Meanwhile, John feels a strange tension between himself and Cara; and Stephen tries to handle a dangerous breakout on his own, but finds himself in over his head.
Stephen and Russell meet a potential new break-out and report back to John about the person, while trying to keep a low profile from Ultra. Later, Russell learns that his dad has passed away; and a shocking secret threatens to destroy Jedikiah's career.
Jedikiah's mysterious boss insists on meeting Stephen when he breaks Ultra protocol. Meanwhile, the Tomorrow People plan to go topside to a party like normal folks, but John and Cara think it's too dangerous; and Stephen makes plans to attend homecoming with Astrid.
Ultra's most wanted, Killian McCrane, resurfaces after years in hiding, and Stephen tries to track him down. Meanwhile, Stephen's mom grows suspicious of his whereabouts which puts him in an awkward position.
Stephen tries to help a classmate in peril and asks John and Cara to assist him, but they make it clear that they don't help humans. Meanwhile, John gives Stephen a mission to infiltrate Ultra's main computer so they can find new break-outs.
Ultra tries to probe Stephen's brain so he looks to his fellow Tomorrow People for help. Meanwhile, Ultra tracks down the identity of a new break-out who uses his powers to commit crimes; and John tries to convince Stephen to spy on Ultra to help save other potential Tomorrow People.
Humans born with paranormal abilities are hunted by a paramilitary group of scientists who believe they are a threat to mankind. In the opener, Stephen Jameson learns that he is one of the Tomorrow People, a genetically advanced race with abilities of telekinesis, teleportation and telepathic communication.