Stephen reluctantly attends a party with Astrid, but is startled when he hears that one of his classmates is in peril. Desperate to help, Stephen turns to John and Cara, but they make it clear that they do not help humans. Stephen secretly tries to enlist Cara’s help, which brings up her own feelings about her traumatic past. Meanwhile, John gives Stephen a mission to infiltrate Ultra’s main computer to help give them an advantage in finding new break-outs.

When Ultra's most wanted, Killian McCrane, resurfaces after years of being in hiding, Stephen enlists John's help in tracking him down. John reluctantly agrees to help, but changes his mind when he learns that Killian isn't after Jedikiah as everyone suspects. Stephen, wants to help, but Cara explains that John's history with Killian, which brings back a flood of memories from John's past, making him do something he never thought he would do again. Meanwhile, Stephen's mom is suspicious of his whereabouts, putting him in an awkward position.

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.

When Stephen and Russell head out for a night of fun, they run into a potential new break-out. Stephen and Russell report back to John and Cara about the new person, but they want to keep a low profile from Ultra. Sadly, Russell learns that his dad has passed away and he is torn about whether or not he should go home. John volunteers to accompany Russell to help keep him out of trouble. Meanwhile, Jedikiah has a shocking secret that could destroy his career.

When Stephen decides to have some fun with his newfound powers, Jedikiah takes extreme measures to make sure it doesn’t happen again. After John and Russell return from their trip, John feels a strange tension between himself and Cara. Stephen tries to handle a new and dangerous breakout on his own, but finds himself in over his head and needing help from his fellow Tomorrow People.

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.

After Stephen returns from the brink, he thinks he has a clue to what happened to his father, but his fellow Tomorrow People are not sure they believe him. When the Tomorrow People learn some disappointing news from John, they make an unexpected decision about their future. The Tomorrow People finally get a lead on Ultra’s secret research lab and they devise a dangerous plan to free all those being held captive there. Meanwhile, Stephen’s mom introduces Stephen and his brother Luca to a new man she is dating, but Stephen is having a hard time getting a read on him.

Stephen and his fellow Ultra trainees are given a test by Jedikiah to see who is worthy of becoming an Ultra agent, but not everyone is happy to work as a team. Cara is faced with a mysterious visitor from her past. Russell is sent on a dangerous recon mission that could force a clash between Tomorrow People groups. Meanwhile, John works with a new break-out.

Stephen feels uneasy about his fellow trainee Hillary who has a secret agenda of her own. Stephen's mom wants the family to go camping including her new boyfriend Peter, whom Stephen seems to be having a difficult time reading. Knowing he is going to be out of town, Stephen asks for Cara and John's help to make sure that everything is ok with Astrid while he's gone.

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.

After getting some shocking news, Stephen attempts to restore order in both his worlds by making a deal with Jedikiah. With a new break-out on the loose, Cara and Russell try to lure him in but must contend with a trap from Ultra. Meanwhile, Jedikiah is closer to developing a new secret technology that could change his future.

Julian is back and angrier than ever, but when he gets caught by Ultra he is forced to strike a deal that could cost his and Stephen’s lives. John once again disobeys Cara’s orders when he learns the Julian has discovered the location of the Tomorrow People’s lair. Meanwhile, Astrid is plagued by nightmares after her near-death experience and turns to her new friend John for some comfort.

Stephen is still walking a fine line with his Ultra partner Hillary, who continues to be suspicious of his loyalties. When the Tomorrow People and Ultra learn that there is a new break-out doing good for humans, they both want her on their side. Meanwhile, Morgan takes a risk and betrays Jedikiah’s trust to help the Tomorrow People, but what Jedikiah discovers from Morgan is an even bigger surprise.

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.