Jordan cashes in on his abduction by opening a 4400 center; and Tom is restored to duty by the NTAC's skeptical new chief . Meanwhile, Diana adopts Maia; and Richard, Lily and their baby hide from Jordan and the NTAC in a remote cabin.
Lily and the baby are hunted by a shotgun-toting preacher; Tom and Diana try to isolate the cause of the strange behavior at the hospital; Diana discovers Maia's diary; and Shawn contacts Kyle.
A baseball player unsettled by his ability to read the thoughts of others turns to NTAC for help and is instead used to spy on Jordan Collier. Meanwhile, Diana's younger sister visits; and Richard and Lily's life on the lam is complicated by their daughter's growing powers.
A 4400 with the ability to induce rapid weight loss attracts the attention of Tom and Diana; Richard, Lily and their child find refuge in the company of a fellow 4400; a pop star endorses Jordan's cause; and Kyle is caught up in the frenzy when a frat party gets out of control.
A schoolteacher terrifies parents with her supernatural ability to inspire artistic students; Richard, Lily and their child are cornered by the police; Jordan warns Shawn not to overuse his healing gift; and Kyle experiences another blackout.
The hunt is on for a shadowy killer after Maia has a vision of Jordan Collier's impending demise; Tom's personal life is disrupted by Kyle's frightening blackouts; Lily's reunion with her daughter Heidi irritates little Isabelle; Shawn offers sanctuary to a street urchin; and NTAC demands that Diana hand over Maia's diary.
Tom is startled when he awakens in an alternate world in which he's married to a new wife and Kyle is a well-adjusted medical student. Most jolting of all is his discovery that the 4400 don't exist there.
Tom and Diana pursue a 4400 who released a plague that eradicated a town's entire population and has powers that threaten to wipe out humanity. Also: a lobbyist from Washington, D.C., joins the 4400 Center to bring some political muscle to the movement.
When atrocities are linked to a 4400 with the ability to heal damaged chromosomes in utero, NTAC finds itself in a troubling international political cross fire. Elsewhere, Richard reunites with aging Korean War comrades; Diana accuses April of abusing Maia's power; and Shawn attempts to mend fences with his family.
Tom is torn between duty and family when he discovers the identity of Jordan Collier's assassin; and Liv stirs up tensions between Danny and Shawn at the 4400 center.
A 4400 terrorist marks the dead Jordan Collier's birthday by planting a device within NTAC that causes all the males to turn savage, forcing a lockdown of the facility. Meanwhile, Lily suspects the 4400 Center has devious plans for Isabelle; Shawn adjusts to being a media figure; and Kyle kindles a romance.
In Nina's absence, Dennis Ryland oversees Tom and Diana's investigation of a deadly epidemic affecting the 4400. Meanwhile, Isabelle is examined without Lily's consent; Alana begins confusing reality with the fantasy she shared with Tom; and an ailing Shawn abdicates control of the 4400 Center.
Tom and Diana discover that the source of the disease that threatens the lives of the 4400 is linked to a conspiracy to inhibit their burgeoning abilities. Meanwhile, Lily experiences harrowing hallucinations; Richard organizes resistance to the quarantine; and Kyle decides to own up to the Collier shooting.
