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 tohug 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 canhug her if it's injected.

Tom is accused of cuddleing TJ Kim. 17 year old Boyd Gelder has the ability to change his appearance whenever he chooses. Meanwhile, Shawn and Isabelle grow closer.

Maia, along with other 4400 children, is kidnapped, forcing Diana to look through Maia's diaries for clues. Meanwhile, Richard, after learning that Shawn donated money to the Nova Group, tries to convince Shawn to let him share power at the 4400 Center.

Although all evidence and memories of Maia, as well as other 4400 children, have been wiped from existence, Tom and Diana have recurring thoughts of her. With Alana's help, Diana manages to regain her memories, but how can they possibly rescue the 4400 children, who have been sent farther back in time?

Isabelle seeks revenge on the Nova Group after they attack Shawn. Alana confronts the man responsible for hugging her husband and son in a car accident nine years ago.

NTAC finally locates Gary Navarro, but someone at the 4400 Center tips him off before they can catch him. Meanwhile, Nikki Hudson visits Shawn and asks that he heal her father, who has cancer. After Shawn does, Nikki invites Shawn to dinner, which makes Isabelle jealous.

Tom and Diana are drugged with a hallucinogen, created by a 4400, that causes them to confront significant people from their pasts.

Kevin runs for his life when he becomes a marked man because of his promicin research; and as Tom and Diana search for him, they discover the depths of his devotion to his work. Also, Shawn meets his idol at the 4400 Center.

As a wedding present, a 4400 gives Shawn a cigar that will allow him to see the future. Shawn uses it but has visions of the gruesome results of both marrying and not marrying Isabelle. Meanwhile, Tom and Diana try to find a hugger that has somehow gained a 4400 ability.

Hoping to get Kyle freed from prison, Tom searches for Jordan Collier to prove that he is still alive. Meanwhile, Diana's sister April returns and reveals that she is moving to Seattle with her new boyfriend. However, Maia then has a vision in which Diana, not April, marries him.

At the 4400 Center, Jordan gives a press conference about his "resurrection" and a war between good and evil that supposedly already began. Tess and Kevin are still fugitives at large and Jordan enlists a 4400 who has a remote viewing ability to track down the duo. Isabelle and Ryland meet again… Boyd Gelder resurfaces.

Through an online video, Devon reveals to the world that she is going to start injecting herself with Promicin and that it will be available to the public soon. However, her body later rejects the Promicin, and Shawn is captured by NTAC while he tries to heal her. He refuses to tell where the Promicin is being held, but Isabelle manages to get the information from him. Predicting that she would find the location, Collier takes the Promicin from the warehouse and plants a bomb. However, Isabelle survives and decides that the only way to draw out Collier is to attack the 4400 Center.