A retrospective in the show in an NBC special. Narrated by Jacqueline McKenzie, "The 4400: Unlocking the Secrets" summarises the events of seasons one and two.
Richard is forced to cope with his infant daughter's sudden transformation into a woman and a horrendous change in his wife, Lily. Meanwhile, Dennis Ryland is injured during Congressional hearings, and the person responsible may be part of a radical 4400 splinter group.
Tom and Diana continue to pursue the Nova Group; Maia starts school at the 4400 Center; Isabelle gains new insight into her role in the future.
Tom Baldwin is arrested by the NTAC for a crime he swears he doesn't remember committing; Shawn guides Isabelle through the things she missed in life due to her sudden transformation into an adult.
Tom and Diana try to foil a kidnapper who's going after 4400 children. Meanwhile, Shawn's past comes back to haunt him.
Tom and Diana continue their search for a mysterious kidnapper who is targeting 4400 children, while Shawn's relationship with Isabelle causes concern at the Center.
When Shawn is attacked by the Nova Group, a shaken Isabelle decides to seek revenge. Meanwhile, a youthful 4400 offers Alana some information about a tragic incident from her past.
Tom and Diana are forced to cooperate with Dennis Ryland in order to find Gary Navarro of the Nova Group, and they soon discover that someone at the 4400 Center may be helping Gary hide out. Meanwhile, Shawn and Isabelle's relationship grows complicated.
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.
Tom and Diana probe a series of gruesome murders. Meanwhile, Shawn receives a gift from a 4400 that lets him see his future.
Tom hopes to clear his son Kyle of murder charges by looking for Jordan Collier, who might still be alive. Meanwhile, Diana receives a surprise visit from her sister April and her new fiancé.
Tom and Diana suspect Jordan's involvement in the breakout of Nova members from NTAC custody. Meanwhile, April's engagement is complicated by a prediction from Maia.
Tom and Diana continue their pursuit of Jordan Collier, whose plan for mankind may have dire consequences. Meanwhile, Dennis Ryland heads back to NTAC.
