The second season of the 4400 begins a year after the events of season 1, not counting the small interlude with Richard and Lily in hiding, and Lily going into labor with her baby.
Since the end of season 1, Baldwin has been stuck behind a desk while Skouris, rotating through a number of incompetent partners, has made little to no progress investigating the 4400. Skouris is also adopting the clairvoyant girl Maia as her daughter, and Baldwin's son Kyle, out of his coma, has been in quaratine for the past year, much to his frustration. Jordan Collier, billionaire and 4400 member, is attempting to build a seperate nation or some such for the 4400, and he's not above breaking the law to do it. His search for Richard, Lily, and their six-month-old baby Isabelle also continues, while Richard & Lily are on the run from the US government, and zealots who believe the 4400 to be a harbinger of doom.