A man runs away, attempting to hide, when Tom and Diana chase him. Tom asks Diana what are they doing here, stating that it is 'so wrong.'
Nina returns to NTAC, Dennis reveals to Tom and Diana that the first of the 4400s here died over night; Diana remarks she is going to quarantine.
Diana and Tom visit Max's office. Diana holds Max at gunpoint.
A flashback takes the episode back to 8 weeks after the 4400 had returned.
Max Hudson explains to Dennis Ryland that the body produces four neurotransmitters and that Orson Bailey produces five neurotransmitters, explaining why he exerts telekinetic properties, essentially a 'backstage pass to the VIP section of the brain' Orson is using parts of the cerebellum no human has access to. Max tells Dennis that all 4400s are producing trace amounts of promicin. Dennis says, 'So it's just a matter of time before every 4400 develops telekinesis. 'Max replies that they may not get telekinesis but they will get something.
The episode returns to the present.
Max Hudson explains to Tom and Diana at gunpoint about the promicin-inhibitor and how he was ordered to synthesize an inhibitor. Diana lowers her gun. He tells her if she is not going to shoot him, then let him get back to work.
Allison visits Kyle's house, telling him that Roy is going to take a plea bargain to avoid the death penalty. He will face life in prison and be ineligible for parole for 20 years. Kyle tells her Roy wont be going to prison.
Tom and Diana visit Kevin Burkhoff and Matthew Ross at the 4400 Center. Kevin tells them that he has figured out how promicin works and that if he can find one 4400 who hasn't been exposed to the inhibitor, he could develop a cure.
Brian brings Lily and Isabelle some groceries. Lily and Brian talk, and Brian tries to seduce Lily. She refuses and Lily slaps him, making Bryan angry, who punches her. Lily grabs a knife in defense and stabs Brian. Brian falls to the floor. Lily's phone rings, and when she answers it, Brian speaks to her. She looks to the floor and "Brian" is gone.
Kevin speaks to Richard and Matthew regarding him being a collaborator. He wonders if they have a 'clean 4400' - one who hasn't been exposed to the inhibitor.
Max Hudson is found dead in his car, apparently suicide. He left a note that mentions a "firewall memo."
Tom returns home and tells Kyle to be ready to leave to go to Spain; Kyle asks if his dad knows that Roy Marsden is going to go to prison for life. As his dad leaves, Kyle picks up a notebook he had hidden, revealing his confession of Collier's murder.
Tom and Diana get a possible lead in their case and go to visit Ryland's old secretary.
Brian brings Lily and Isabelle back to the 4400 safe house, where Richard is. When Kevin sees Isabelle, he asks, 'Is that her?
Tom and Diana visit Dennis Ryland's old secretary. She has been expecting someone to visit her, and she asks if there here about 'Firewall.'' She gives Tom and Diana the documents.
Kyle tells his father that he is going to confess to the murder of Collier. Tom tells him not to say anything until he gets back.
Kevin explains to Richard and Lily about the 'cure' he has created using Isabelle's blood. However, there is only enough for one shot. Richard says that if they can get it into quarantine, one shot will be enough.
Nina tells Tom and Diana that a 4400 safe house has been exposed. As Tom and Diana head for their car, Kevin Burkhoff tells them that he has brought something for them. He tells them whatever they do, don't drop it.
Dennis Ryland and his men arrive at the 4400 safe house. He gives them an ultimatum: if they do not comply, they will come in with force. Tom arrives and tells Dennis he knows about Firewall.
At NTAC quarantine, Diana tells Shawn that she has brought something that will help him, although she would rather give it to Maia. Diana helps Shawn get up; Shawn puts his hands on Maia to heal her.
Tom arrives at NTAC quarantine and finds a healthy Alana, who tells him it was a miracle. He sees Shawn up and walking around, and smiles at him.
Twenty-four hours later, Tom brings Alana home. Kyle goes to the 4400 Center to see Shawn, telling him that he killed Jordan Collier. Shawn is distraught, but he uses his ability on Kyle to rid him of the evil in him. It appears to work.
Marco and Diana have a drink at Diana's home. Maia comes into the kitchen and tells them that nothing is over; it's just beginning.
Kyle prepares to turn himself in to the authorities for Collier's murder. At NTAC, Dennis places Nina Jarvis's desk plaque on her desk and leaves her office after being arrested and handcuffed. Kevin injects himself with Promicin. Richard reaches for a glass, which comes toward him; he is developing telekinesis. Lily finds that Isabelle has disappeared.
The episode ends with a woman walking into Shawn's dining room, saying 'Hello Shawn. I'm Isabelle.' A man appears on a beach wearing tattered clothes; although he is disheveled and has a beard and long hair, it is obviously Jordan Collier.