Stephen can suddenly teleport, do telepathy and telekinesis, like the voice in his head Cara, and others living underground. His missing father was their leader. His uncle Jed heads Ultra, who find and kill them or take their powers.
Stephen plants a computer virus for sending breakout locations to the rebel stolen supercomputer Tim, but Jed sends an ambush and traps Cara. Stephen offers to inject her with Ultra's power-removing serum. Cara reveals how her powers came.
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, is making him do something he never thought he would do again. Meanwhile, Stephen's mom, Maral 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 to.
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. Meanwhile, Stephen has a moment of clarity when it comes to his father, and is more determined than ever to figure out what happened to him.
Stephen (Robbie Amell) 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 (Mark Pellegrino) head. Meanwhile, Cara (Peyton List) and Russell (Aaron Yoo) 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.
Something seems a little off... 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 have a difficult time reading. Knowing he is going to be out of town, Stephen asks for Cara and John to make sure that everything is okay with Astrid while he's gone.
Stephen is left to face The Founder due to Jedikiah. To protect Astrid, he has to make a dangerous deal. Cara issues a harsh and unexpected punishment to John when they clash. A surprising secret about Stephen's mom is revealed.
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 breakout 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.
Both Ultra and The Tomorrow People track a breakout who is flaunting his powers as a street magician. Jedikiah has fled Ultra and tells Luca of Stephen's powers. Meanwhile The Leader announces the genesis of a kinder and gentler Ultra.
The Founder requests a summit with The Tomorrow People. Cara agrees but only if Hillary is held hostage. Ultra agents find Jedikiah's hideout, but with John's help, eludes capture. Stephen attempts to reach Roger using the machine at Ultra.
With the possible return of Roger on the horizon, everyone is concerned about the consequences if The Founder were to find out. Now aware of the truth about the machine The Founder has been using him to train in, Stephen 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.