A returnee exhibiting telepathic abilities seeks help from NTAC, but is instead used as a mole to infiltrate Jordan Collier's 4400 Center.

A morbid premonition from Maia threatens the future of the 4400 Center.

A 4400 with the ability to repair damaged chromosomes hides a shocking past. And while Richard seeks out a tormentor among his Korean War buddies, Shawn reconnects with his family and tries to help Kyle.

A 4400 terrorist releases a signal at NTAC that makes the men violent, forcing a lockdown of the facility. Lilly questions how the Centre is handling her daughter, and Shawn tries to recruit a familiar face.

Discovering that NTAC is behind the disease plaguing the 4400s, Tom and Diana try to get to the bottom of NTAC's cover-up, while Kyle considers turning himself in.

Ryland and other government officials are on trial for withholding vital information that they discovered about the returnees when a disturbing sound is heard the courtroom. Tom and Diana, with the help of Gary Navarro, try and track down T.J Kim, who they believe is responsible for the piercing sound heard in the courtroom. Richard and Lily are forced to deal with a now grown Isabelle While Lily also suffers from a rapid aging disease that Shawn is unable to heal. Tom and Diana also investigate a radical organisation called the Nova Group that appears to have ties with Shawn and the 4400 Center.

Gary Navarro is arrested for the second attempt to assassinate Dennis Ryland. Knowing she is the key to her mother's survival, Isabelle attempts to kill herself by jumping off the 4400 center building only to survive without a scratch. Matthew Ross expresses his displeasure at her actions and tells her of the destiny she is to face. Isabelle is troubled about what Matthew told her, but after a discussion with Shawn she decides it's her choice with what she does with her life. Matthew gives Isabelle a substance that can kill her if it's injected.

Tom and Diana continue to investigate the disappearance of the 4400 children. Isabelle and Shawn's relationship becomes public.

Tom and Diana are drugged with a hallucinogen, that was created from oil that was secreted from the hands of a 4400.

Tom and Diana's investigation into a series of gruesome murders leads them to uncover another conspiracy within the government. At the 4400 Center, Shawn receives a gift from another returnee that allows him to see his future.

NOVA group members that were in the custody of NTAC escape from jail with outside help from Jordan Collier. Diana tells April about her relationship with Ben. Shawn and Richard learn that Isabelle is working with Dennis Ryland.

Tom and Diana search for someone who has the ability to make people's worst fears come true. Danny seeks Shawn's help to find a promicin shot. Meanwhile, Cassie leads Kyle to a book that contains a prophecy about Jordan Collier.

Tom tracks Jordan to a small town, where he meets a woman who can relieve people's stress by talking to them. Meanwhile, Marco and Diana have a nice talk. Maia's visions are giving her nightmares.

Jordan Collier's movement takes a huge step forward when his followers settle in the heart of Seattle.

Richard surprises Isabelle when he shows up in Promise City but the happy reunion takes a turn when Richard kidnaps her in hopes to start a new life with his daughter.

Tom and Diana must race to find the source of a computer virus that could bring down Ubient software, one of the world's largest software companies that is run by suspected member of the marked, Drew Imroth. Meanwhile, Maia visits Promise City where she receives an unexpected birthday surprise: a visit from her birth parents.