At Ultra, John is strapped to a table and told by The Founder that he must tell them where all the other paranormals are. Of course he says nothing and the torture begins. The Founder comes close to strangling John and Stephen steps in to put a stop to it, giving The Founder a chance to force John to admit that he killed Stephen's father.
Cara and Russell come up with a plan to kidnap Morgan to trade for Morgan and they track her down to a cabin. She fears they are there to take her powers and tries to run, but of course Cara is able to catch her. Cara goes to Jedikiah and makes him the offer: Morgan for John.
Stephen goes to see John and asks why he killed his father and John tells him the whole story. Stephen calls John a fraud to lying to all of his people so long. Stephen tells John he'll forget it all for now because Thanatos is real and he's more sure than ever that his father is alive. He tells Stephen that he's going to get him out.
Back at home, Stephen asks his mother if she knew about the Thanatos project, she only says to let it go and that they are better off, and safer, without him.
Jedikiah goes to see John and says he's there to say good bye. Gives him a kiss on the forehead and everything, but John spits in his face. Jedikiah calls Stephen to his office and shows him the video of taking away Cara's powers and accuses Stephen of stopping time to let Cara keep her powers. Jedikiah says it's pardonable because he knows Stephen loves Cara, admits that he's grown attached to a paranormal.
Jedikiah tells Stephen the he has to be the one to let John free as he can't do it himself. Stephen goes in to give John his last meal and John breaks out of his cuffs. Turns out Jedikiah's goodbye kiss was a distraction to hide giving John a key. With Stephen's help, John escapes.
With John home, Cara returns Morgan to Jedikiah but he wants to them to take Morgan and protect her. He knows the Founder will sift his brain and she will be safer if he doesn't know where she is. Back underground, John and Stephen are teleporting over and over so that Stephen can try and stop time and get back to limbo, but it's not working.
Cara notices that John is acting differently, but doesn't know why. John wants to tell her the truth, but Stephen says it's not worth it and it will only hurt her. Besides, Stephen says, his father is still alive. But John is still guilty over lying for so long.
Back at home, Stephen gets his mother to give him the last of his father's belongings, including a box of research notes.
At Ultra, the Founder presses Jedikiah and he admits to his relationship with a paranormal. He even goes so far as to call it an affair of the heart. The Founder asks if he will need to take care of the "loose end" but Jedikiah says he will do it.
Stephen goes through his father's box and find a video of his father and Crick working on their experiments. John takes Cara away to admit to her the truth about killing Stephen's father. She accuses him of never being honest and even says the reason she ended up with Stephen was because John was never fully with her.
Stephen watches his father's video and sees them do the experiment over and over with no results, until his father suggests they try the "alternate method." Stephen goes to see the professor and tells him what happened when he drowned. Crick says it's possible he was in limbo, but it was also possible that his father didn't want to be found. As they are talking, bullets riddle the cabin and the professor is killed by the Founder before he can say more.
Stephen goes back underground and tells them the only place he can find his father is in between life and death and that John must try to kill him. Stephen tells John that his father planned it all and wanted John to kill him so that he could stop time at the moment of his death. They of course don't want to believe him, but he points out that they tracked him down because they thought he was the chosen one so they need to trust him.
Back home, asks his mom if he can have some friends over for dinner. She asks if he found anything in his father's box and he lies and tells her he didn't.
Jedikiah gets home and Morgan meets him there.
At Stephen's party, the Tomorrow People mix with Astrid and his mom. Astrid knows that something is up and Stephen admits that he's going to try and bring his dad home so he might be gone for a while.
Jedikiah leaves Morgan's bed to get a pillow and proceeds to put a pillow over her head and shoot her dead. Back at Ultra, the Founder reads his mind to ensure he did as he was told. The Founder warns him that he's still not completely pardoned. If it weren't for Stephen, the Founder would have little use for him and urges him to bear that in mind as they groom Stephen for his ultimate purpose.
Back underground, Morgan is there safe and sounds. Turns out Jedikiah only faked killing her to keep her safe.
John is prepping to inject Stephen so that his heart slows. Stephen asks John to promise to take care of his family, then tells Cara to let John off the hook. He points out there their kind is hanging on by a thread and they are all vulnerable when Cara and John are at odds with each other.
John injects Stephen and when his heart stops, Cara loses contact with him. With only one minute left to go before brain damage, Cara wants to bring him back but John stops her, saying it's what Stephen wanted. She gives him the drug and Stephen finally awakes with one message: he saw his father and they have to find his body.