Daniel Armand of The Nova Group launches an attack against Shawn causing mental illness. Isabelle seeks retribution. Alana tracks down a drunk driver responsible for the death of her husband and child.
- Tom has been plagued with bad dreams since he made his deal with the future to kill Isabelle in exchange for the return of Maia and the other children. In his dream, Isabelle tells Tom that she is evil and will be responsible for the deaths of billions of people.
At The 4400 Center, Shawn suffers from the mental illness inflicted upon him by Daniel Armand, a member of the Nova Group. Tom and Diana are called in to investigate. But with no real lead on Daniel Armand or a cure for Shawn's illness, Richard is forced to commit Shawn to a mental institution.
Impatient with NTAC's progress, Isabelle decides to pursue Daniel Armand on her own. But as she packs to leave, Matthew Ross tries to talk her out of it. He explains to Isabelle that not everyone in the future feels that the 4400 are a good thing, and that Shawn being sick is actually a positive turn for their agenda.
Matthew reminds Isabelle of her mission. She is here to eliminate the 4400. But Isabelle's feelings for Shawn are more important to her right now than any mission. Matthew continues to object so Isabelle kills him. She then proceeds to break Shawn out of the mental institution where he is being held. Isabelle, with a sick Shawn at her side, sets out to find Daniel, leaving Tom and Diana to follow the trail of dead Nova members she leaves behind.
Isabelle eventually tracks down Daniel Armand and forces him to cure Shawn. She urges Shawn to take revenge and kill Daniel, but he refuses. So, Isabelle decides to take revenge for Shawn, and forces Armand to use his ability to give himself a mental illness. Since no one witnessed any of the Nova members or Matthew's murder, Isabelle isn't arrested. But Tom knows she is guilty.
Later that night, Tom confronts Isabelle with the syringe and reveals that the future wants him to kill her. Isabelle rolls up her sleeve and offers Tom an opportunity to inject her. But Tom can't go through with it. He's not ready to become a murderer.
The next morning Isabelle, now free from Matthew's guidance, embarks on a new agenda that starts with her going to see Dennis Ryland.
In other goings on, a teenage 4400 reveals to Alana the identity of the man responsible for the hit and run that killed her husband and son nine years ago -- Keane Driscoll. Alana finds Keane leading an AA meeting. He's been clean and sober for nine years.
Alana eventually confronts Keane. He admits he thought about going to the police after the accident. But he felt that committing himself to sobriety and helping other people stay clean was a more useful penance than sitting in as jail cell. Alana decides not to turn Keane in. Keane is so guilt ridden by the encounter that he turns to drinking and ends up in a car accident that leaves him in critical condition.