When a passing comet abruptly changes course and hurtles towards Earth, there is widespread panic and distress as people prepare for Armageddon. However, the comet does not crash: instead, it slows down, hovers, and eventually touches down on a lake in the Pacific Northwest.
Finally, 4400 people emerge from a blinding white light, people from all different ages and walks of life who have been presumed dead or missing -- and none aged even a day from when they were last seen. It's as if a giant time capsule full of people has been opened up, unaltered and untouched by time.
Although not immediately evident, it soon becomes apparent that The 4400 have each been returned with a special power as they unwittingly begin to exhibit abilities including superhuman strength, healing touch, and clairvoyance. Eager to revisit memories from their past and reunite with those they left behind, two worlds collide as 4400 people acclimated to living in the past are forced to deal with the new challenges of living in the present.
A new federal division agency of Homeland Security called NTAC (National Threat Assessment Command) is formed to follow The 4400, lead by Tom Baldwin, a crime investigator, and Diana Skouris, a bio medic. Tom's involvement is personal: his nephew Shawn was one of the 4400 people abducted - and, if not for Shawn, his son Kyle would have been abducted instead.
Building their investigation case by case, Tom and Diana slowly begin to shed light on the mystery of the 4400. Finally, on the very beach where Shawn was abducted, they learn the truth about what happened: The 4400 were not abducted by aliens, but instead were taken by humans living hundreds of thousands of years in the future. Facing an end stage of human evolution and with a vested interest in the betterment of their predecessors, they have sent back The 4400 to play pivotal roles in upcoming events that will impact the future of mankind.
One year after the events on the beach revealed the 4400 were taken and returned by future humans, the world is a much different place. After a period of intense medical observation, Tom has returned to NTAC in a limited capacity, assigned only to desk duty.
He eventually secures his son's release from a similar government study and is excited by the prospect of returning to a somewhat normal life. However, professionally, he's also anxious to re-team with Diana and get back out in the field. Diana, having been through a series of inept partners, finally finds a way to cut through the red tape and get Tom back, all while in the midst of formally adopting Maia.
Meanwhile, Richard, Lily, and baby Isabelle -- who is now six months old and showing that she is far from an ordinary child -- are still living in meager conditions in a mountain cabin far away from Jordan Collier. Collier has now closed Arcadia Estates, his mansion and compound for The 4400 refugees, and is on the verge of opening "The 4400 Centers," a place for non-members of the 4400 to discover "the 4400 within themselves."
Collier and Shawn have developed a strong father-son bond after Shawn healed Collier from the detrimental effects he suffered after touching Lily's stomach/womb. Collier becomes Shawn's guardian, and enlists him to heal important benefactors of The 4400 Centers.
With the world understandably curious about The 4400, rumors begin to spread about their mysterious abilities, and public opinion soon becomes divided between those who embrace The 4400 and those who fear them. As the members of The 4400 struggle to resume and rebuild their "life interrupted," each will come to play a pivotal role in events still to come ... events that will shape the destiny of the human race.
The third season sparks a new beginning for the 4400 people who, over a span of years, mysteriously disappeared -- only to be returned to Earth all together in a ball of light. Though the returnees had not aged physically, many of them reappeared with dramatic abilities ranging from enhanced reflexes to precognition. NTAC (National Threat Assessment Command) is the government agency responsible for keeping track of the returnees and investigating all things related to the 4400.
The premiere picks up mere seconds after we last saw a year-old baby, Isabelle, become a beautiful twenty-year old woman. Her father, Richard, is forced to deal with his daughter's sudden transformation -- and an even more surprising change in his wife, Lily. Meanwhile, Tom and Diana pursue a radical 4400 organization called the Nova Group that has launched attacks against Dennis Ryland and the other bureaucrats involved with the inhibitor scandal. At the 4400 Center, Shawn is forced to contend with the new Nova threat and the interests of Isabelle.