When Stephen Jameson begins hearing voices and waking up in strange places, he starts to question his sanity. In desperation, Stephen decides to listen to one of the voices in his head, and it leads him to his first encounter with the Tomorrow People — John, Cara and Russell — a genetically advanced race with the abilities of telekinesis, teleportation and telepathic communication. The Tomorrow People inform him that they are being hunted down by a paramilitary group of scientists known as Ultra, led by Dr. Jedikiah Price. Meanwhile, Stephen gets another surprise that leads him down his own path, which he hopes will help him uncover the truth about his father’s mysterious disappearance.

When Ultra tries to probe Stephen's brain, he looks to his fellow Tomorrow People for help, but is rebuffed by an angry John, leaving Cara to go behind John's back to help Stephen. Meanwhile, Ultra tracks down the identity of a new break-out, who has been using his powers to commit crimes. Stephen tracks down the new break-out, but is shocked when an Ultra swat team is called in. At a loss for what to do, Stephen calls on John, Cara and Russell for help, leaving them with a risk of also getting caught. Upon learning of Ultra's evil motives, John tries to convince Stephen to spy on Ultra to help save other potential Tomorrow People, while still pursuing the answers he seeks about this father.

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.

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 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.

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.