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.

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.