The 4400 tells the stories of 4,400 abductees after they are returned to earth. In the words of the executive producers, these are stories of people dealing with traumatic changes, driven by the mystery of what happened and why. Some of them have been affected in mysterious ways, and some will have certain abilities, both good and bad, so part of the drama will be watching them adjust to these changes within themselves. The series kicks off with a ball of light sailing toward Earth, but rather than the expected catastrophic event, thousands of returned abductees are left with no memory of their otherworldly experiences. Each has been gone anywhere from a few months to several decades but none has aged a day.
7 of the 4400 have died and Maia gets worse all the time Out of suspicion and despair Diana threatens Dr. Hudson with a gun. Lily has run away with Isabelle and Richard pleads he to come back. Marsdem seems unable to avoid a long prison term which makes Alison contact Kyle.
Tom and Diana continue their investigation on Jordan Collier's plan for mankind. Dennis Ryland rejoins NTAC. Isabelle prepares for battle.
Paramedics try to resuscitate Susan Farrell. They believe that she took promicin and lost the 50/50 lotto that comes with it. Danny is certain that she did not take the shot. After arriving at the hospital with the paramedics, things get complicated as everyone around Danny start to die. Garrity and another NTAC agent are sent to the hospital to assess the situation.
Everyone on Earth is excited about a comet passing by, but as soon as its trajectory changes to a collision course, everyone starts to panic. The comet turns out to be a giant ball of light that, after exploding, leaves behind 4400 people. They are missing persons who have been gone from a few months to 60 years, and none have aged a day. The 4400 are put in quarantine and eventually released. Some of the returnees begin to exhibit strange and uncontrollable new abilities. Tom Baldwin and Diana Skouris, two Homeland Security agents, are appointed to find out what happened to the 4400.
An elderly woman develops the ability to astral project unseen by others, but she is stuck in limbo when her body is murdered, and she must find a way to contact Tom and Diana to help catch her killer. Elsewhere, Shawn decides to start healing people again despite threats.
Maia sees a vision of Jordan Collier's death. Kyle's frightening blackouts are disrupting Tom's personal life. Diana is asked to hand over Maia's diary to NTAC.
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.
A high school student develops an ability after injecting promicin. Tom visits Isabelle in jail, while Diana searches for her missing sister. Following the advice of a young woman, named Cassie, Kyle is able to wake Shawn from his coma. Jordan Collier's conscience gets to him. Meanwhile, NTAC gets a new director.
Tom is furious upon finding out that Lyttel took his son Kyle into custody. Diana offers him help in getting Kyle back. Meanwhile, Richard suspects that Collier is trying to take control of Lily's life, and as soon as Collier reveals his intentions, Richard and Lily leave Arcadia Estates. Elsewhere, Danny snaps at Shawn when he finds out that he and Nikki have slept together. Tom and Diana finally find out what really happened to the 4400, which leaves a disturbing question: is this the end - or just the beginning?
When Jordan Collier and his followers seize control of most of Seattle, the government sends a Delta Force of enhanced soldiers to capture Collier dead or alive.
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 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.
A school teacher terrifies parents with her supernatural ability to inspire artistic students. Meanwhile, Richard and Lily are confronted by police, and Jordan warns Shawn not to overuse his healing gift.
April's new ability takes her in a danger. Meanwhile, Shawn is approached to run for public office. Kyle helps Isabelle.
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 wants Shawn to rejoin the movement. Meanwhile, a 4400 with an amazing ability disappears.
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.
Richard returns from hiding to abduct Isabelle from Promise City, hoping to "start over." Meanwhile, Tess, her schizophrenia out of control, uses her ability to take control of a diner full of people.
Tom and Diana are sent out to investigate a homicide that resembles the MO of a serial killer who was never caught nor heard of for 21 years. The first suspect is Oliver Knox, a member of the 4400. However, Knox has an alibi for the night of the murder and another man confesses to all the crimes. Tom and Diana suspect that Knox is luring people to kill for him and try to lay a trap on him. Meanwhile, people begin to turn hostile toward the 4400, and Jordan Collier decides to organize his fellow returnees. But Richard feels uneasy about Collier's interest in them.
Tom and Diana track down a man to a museum, and during the chase, Tom finds a mysterious lab that only he can see. Later at the office, Tom finds that all his 4400 case files are gone, and no one has ever heard of the 4400.
Tom and Diana are drugged with a hallucinogen, that was created from oil that was secreted from the hands of a 4400.
Tom is accused of murdering TJ Kim. 17 year old Boyd Gelder has the ability to change his appearance whenever he chooses. Meanwhile, Shawn and Isabelle grow closer.
Kevin Burkoff becomes a marked man when his research on promicin is discovered. When Tom and Diana search for him, they discover how far he will go to protect his work. Shawn meets his idol at the 4400 Center.