In a flashback to six years ago, John is being hooked up to machines to be the first candidate of some sort of experiment. Jedikiah admits that is worried about him, but claims it's only because he's afraid to lose his best agent. The experiment quickly goes wrong and we see Jedikiah waking up in a sweat next to Morgan.
Jedikiah and Morgan talk about the day they met when she using her telepathic abilities to pose as a psychic. Jedikiah appears to really care about her and decides that he must leave as he's already stayed too long and possibly put her in danger.
Back underground, Stephen is still trying to figure out what "Thanatos" means. Cara comes up with a plan to read Jedikiah's mind while he sleeps. John is skeptical, but lets Cara and Russell try it. They go to Jedikiah's home, but Cara only barely gets into his mind when Jedikiah wakes up. She's able to jump away, but when Russell tries, Jedikiah is able to hitch a ride and ends up in the underground cave.
They immediately knock him out and while he's down, Cara argues that she wants to try and get back into his head. John's afraid Jedikiah will figure out she still has her powers, but again decides to let her try. She asks Jedihiah what "Thanatos" means, but he says he will only speak to John. Because Jedikiah had a telepath as a brother, he learned a trick or two and Cara can't get into his head.
Once alone, Jedikiah tells John that he has to get him out or John's friends will learn all of John's secrets. In flashback, Jedikiah asks John to kill a man who was a criminal. John hesitates but takes the gun and fires the trigger but it was loaded with blanks. Turns out it was all a test to see if he could kill and he passed. John is then given his real assignment.
In the present Cara admits that she saw and felt what Jedikiah did for John and that Jedikiah loved him like a son. Back at Ultra, John sees that a team called the Brain Trust has been put on the case. They are looking for Jedikiah's specific brain signature. The man running the Trust is called "the Founder," as he founded Ultra. The Founder was also the voice Stephen heard when he was in the mansion.
Stephen goes back underground and says they need to get Jedikiah out or they will all be in danger. Cara asks for a little more time. She saw Morgan in Jedikiah's head and asks Stephen to send Ultra after Morgan.
Jedikiah mouths off to Cara and when he mentions a near-rape experience of hers, she loses control and beats him until John pulls her off. Cara tells John that Jedikiah still cares about him and is hiding something to protect him. In the past, we discover that John's orders are to kill the man who trained him. He is the only one with paranormal skills, plus the ability to kill, who can do it.
In the present, John tracks down Morgan and follows her when he sees her jump. But when he realizes the extent of Morgan and Jedikiah's relationship, he hides her from the Ultra team and tells her to run.
Back underground, Cara, Russell and John finally get Jedikiah to talk by telling him they know about Morgan. He tells them "Thanatos" is a man named Professor Aldis Crick who worked with Jedikiah and Stephen's father. Crick helped them with experimentation but that's all he will say. Irene volunteers to help track down Crick and talk to him.
At Ultra, The Founder is angry that they've lost Morgan's signal and still haven't found Jedikiah. Plus, they can't seem to find Stephen. The Founder decides to plug himself into the machine to look faster.
John, Irene, Stephen go see Crick. He says the original purpose of Ultra was to help people with use of paranormals. John finds out his father could also stop time and that Jedikiah was once a good man but was influenced by The Founder. They also find out there is a place in between times called "limbo" and Stephen thinks he was there when he spoke to his dad and that he just needs to find it again.
Underground, Russell gives Jedikiah his dinner and Jedikiah fools Russell into thinking he's choking and attacks. Cara is forced to use her powers to save Russell but tells him that found an antidote to the serum. But she tells John that Jedikiah doesn't seem to be buying it and they both know that if he gets out Stephen is dead. Cara suggests that maybe he never gets out. Suddenly she doesn't have as big of a problem with Stephen's ability to kill people.
Meanwhile The Founder gets closer to finding Jedikiah and as Ultra get closer, John says he knows what he has to do and jumps with Jedikiah. Once they land Stephen pulls a gun on Jedikiah. In a flashback, John confronts the man he was sent to kill and we see it was Roger, Stephen's father. Despite Roger's protests, John shoots him.
In the present, John fires his gun repeatedly, but doesn't kill Jedikiah. Ultra arrives and John tries to fight them off but he can't beat them all. Jedikiah stops them from continuing to beat him but they drag John back to Ultra. In the past, John apologizes to a dying Roger and promises that he will find his son and protect others like them. Roger dies in John's arms.