Episode opens with John and Cara fighting to save Stephen, who is chatting with his dad in Limbo. They pull him out before he can get more than one thing from his father: Find Simon Plane. Stephen tells them what hid dad said, but Cara can't read it in his mind and thinks he's imagining things. John is actually inclined to believe the experiment might have worked.
Back at home, Stephen goes home to find his mom has a new boyfriend. Seems she's finally moved on after 10 years. Underground, John is getting a hair cut from Morgan and there seems to be some definite flirting there, but if Cara notices, she doesn't say anything. They start out arguing about what Stephen saw and end up arguing about whether John should tell everyone he killed Stephen's father. He wants to do it, she doesn't.
In what appears to be a mental mental hospital/prison for paranormals, Errol (guest star Ty Olsson) uses the severed hand of another patient (freely offered) to escape.
In Ultra, Stephen meets the ALICE, an AI computer. When he tries to access it for Simon Plane, she calls Jedikiah. Stephen says he read the name somewhere, Jedikiah says her dad was crazy at the end and it means nothing. They get the call about the escape and Stephen goes with his partner to pick up Errol, but the man is too powerful and escapes.
Back underground, John has told the group what he did to Roger and vows to continue to look for their old leader in Limbo. Many of the group aren't happy and Mike nominates Cara as new leader. They put it to a vote and Cara wins.
After the vote, Stephen tells them them about Errol's escape. Turns out they know all about the Citadel. When Stephen says Errol pushed him out of his head, Cara understands how powerful he is and why Jedikiah would want use him. They decide to rescue Errol and use him to find out the location of Citadel and rescue the paranormals being held there. Everything goes to plan, but they decide Stephen has to take a bullet or Jedikiah won't believe he wasn't in on it. John shoots him in the shoulder and they escape with Errol.
The plan works and Jedikiah is happy that Stephen has literally taken a bullet for Ultra. Underground, Errol is acting unpredictably. He has blocked most of his memories of the Citadel, but Cara goes inside his mind and gathers enough clues to lead them to a location. John wants her to slow down, knowing that Jedikiah is on high alert. But she decides to go in anyway and leaves John and Tim behind as her eyes and ears. She also wants John to guard Morgan, so that they can use her as leverage against Jedikiah if necessary.
Back at Ultra, Jedikiah seems suspicious of Stephen, but doesn't come out and say it. Under the pretense of caring for his nephew, he orders more pain meds for Stephen. Jedikiah announces that he thinks the paranormals are looking for the Citadel, just as Stephen goes under and can't warn Cara. Stephen is out for a while, but manages to wake up and warn John but it's too late, the paranormals are already at the Citadel.
They try to break out the prisoners, but Ultra is overriding the system. Cara orders everyone else to leave, but stays behind and manages to break one girl out of her cell. Jedikiah catches them before they can escape and a standoff ensues when neither of them will back down. She says she will kill Morgan and he says he's already said his goodbyes. Errol jumps between them to try and save the girl, but Jedikiah kills him and the standoff looks like it will end with Cara's life. Then John jumps in and holds a gun on Jedikiah, who realizes that the reckless plan was Cara's. Jedikiah lets Cara and the girl go, but not before John tells his former boss that if Cara ever orders him to kill Jedikiah, he will.
Cara goes to get Morgan and wants to kill her. John says no, they can't play by Jedikiah's rules. If she can't see Morgan is one of them then she is lost as a leader and they are lost as a people. She backs off.
Back in Ultra, Stephen wakes up in his hospital bed and finds out Jedikiah told his mom he fell asleep at his desk to explain his extended absence. Jedikiah once again acts suspicious of John shooting Stephen, but not making a kill shot. Stephen says he sick of it and has earned the truth. He asks Jedikiah for the truth about Simon Plane. He was another student of the professor. When Stephen's was killed, Simon broke into the building and tried to take his father's corpse. Jedikiah says he killed Simon and cremated Roger's body himself.
Stephen tells Cara and John what he found out, but John doesn't buy it. He says there's no way Jedikiah incinerated his own brother. Russell agrees and Stephen starts to believe it, but Cara says she's not sure. Cara isn't happy about her first day on the job and Stephen gives her a pep talk to point out what she did right.
In the end, Stephen comes home to find Peter there and when Stephen tries to read Peter's thoughts he discovers he can't.