Writer: Robert Hewitt Wolfe, Director: Nick Gomez
A series of bombings threaten the 4400 after their names and addresses are made public by a journalist named Barbara Yates. As Tom, Diana, and Ryland try to stop the bombings, Tom must also deal with the erratic, disturbing behavior of his newly-awakened son, Kyle, while Diana also struggles to be a good mother to Maia. Their work is complicated even further by the arrival of the aggressive and ambitious Warren Lyttel, an agent from Washington who threatens to take over responsibility for the 4400. In response to the explosions, Jordan Collier, the charismatic leader of the 4400, tries to provide his fellow returnees with a safe and secure place to live. Richard and Lily, now bombed out of their apartment, join Jordan, but question his motives and judgment as the bombings intensify. Meanwhile, Shawn and Nikki's relationship heats up with a fire of its own. As the bombings get more frequent and dangerous, Tom and Diana race against time to prevent the 4400, including Richard, Lily, Maia, and Shawn, from being swept away in the flames.

Writer: Scott Peters, René Echevarria,Director: Yves Simoneau
A comet that was supposed to harmlessly fly by the Earth suddenly changes course, so the extinction of mankind seems imminent. Countries around the world launch missiles to destroy it before it can destroy the planet, but the missiles have no affect because this is no comet. The ball of light enters the atmosphere, and it slows, hovers, and eventually touches down. Soon after, the light shrinks to an intense point, then explodes outward in a concussive burst, leaving behind 4400 men, women and children of all ages. All are missing persons who have been gone anywhere from a few months to 50 years and none have aged a day. The 4400 are quarantined, and eventually released back to their families. As they begin to try and reconnect with their old lives, not all is well: soon after their release, some of the returnees begin to experience unexplainable, and uncontrollable new abilities. It's up to Tom Baldwin and Diana Skouris, two Homeland Security agents, to unravel the mystery behind the 4400.

Writer: Craig Sweeny, Director: David Straiton
A homicide in rural Washington resembles the work of a serial murderer who was active 25 years ago. Tom and Diana investigate a connection between the murder and Oliver Knox, a member of the 4400 who recently resurfaced in the community. When another man confesses to all of the murders, the case seems to be solved. The killings continue and with each murder, another person confesses to the crimes. Forced to contend with the possibility that Knox is somehow convincing his neighbors to commit murder on his behalf, Tom and Diana lay a trap that they hope will prove Knox is complicit in the killings. Meanwhile, public sentiment toward the 4400 begins to turn hostile, so millionaire Jordan Collier seeks to organize his fellow returnees. After Shawn, Richard, and Lily attend a meeting hosted by Collier, they all find themselves involved with Collier. However, Collier's interest in Lily makes Richard uncomfortable - why is Collier so eager to insinuate himself into their lives? Elsewhere, Tom receives news that Kyle's condition has begun to deteriorate, he is forced to confront the possibility that his son may never wake up from his coma. But Shawn's conversations with Collier convince him to explore his abilities, and when Shawn learns that Kyle might be dying, he visits the hospital. Shawn touches his cousin, and he is able to rouse Kyle from his comatose state.

Writer: Ira Steven Behr, Director: Helen Shaver
Tom and Diana investigate a vigilante is a member of the 4400. It seems that Carl Morrissey has been a loser his whole life, but after missing for 18 months, Carl discovers that he now possesses enhanced reflexes and strength. Carl uses these skills to wage a one-man war against crime in his neighborhood, becoming a hero not only to himself but to his wife as well. But fighting crime can prove deadly, even for a member of the 4400. Meanwhile, Richard and Lily move in together. As Richard lookd for work, he must also deal with a pregnant Lily's claims that the unborn baby, is able to communicate its feelings to her. Elsewhere, Shawn and Nikki's attraction to one another continues to grow in spite of Danny's growing suspicions, Meanwhile, Diana finds herself growing close to Maia. Concerned about Maia's life in quarantine, she invites the girl to move in with her.

Writer: Scott Peters, Director: Tim Hunter
Tom is livid when he finds out that Lyttel has unexpectedly taken his son Kyle into custody. Diana, who is having her own problems dealing with Maia, helps Tom break Kyle out of Lyttel's grasp. Meanwhile, Richard is upset when he suspects Collier is trying to take control of Lily's life. Soon after, Collier reveals his true colors, prompting Richard and Lily to leave Arcadia Estates and Jordan Collier behind. Elsewhere, Danny is convinced he can win Nikki back but his effort backfires. Eventually, he comes to learn Nikki and Shawn have slept together, provoking a fight that results in Shawn leaving home. As the lives of the 4400 intersect in unexpected ways their storylines move toward thrilling conclusions, Tom and Diana find themselves on the beach where Shawn was taken. In an emotional and powerful moment, they finally learn the truth about what happened to the 4400. It's a remarkable revelation, but leaves one troubling final question: is this the end - or just the beginning?