What looks like a comet is on a collision course with the earth -- but then it manoeuvres, and turns out to be some sort of spacecraft. From it, 4400 people who had disappeared over the last 60 years all suddenly return, with no memory of what has happened, but with strange new powers (precognition, playing with life forces, crushing skulls from afar, etc). Tom Baldwin and Diana Skouris are agents from Homeland Security charged with investigating the returnees: Tom's nephew Shawn is one of them, and his son Kyle has been in a coma for the three years since Shawn was abducted. Lily discovers she is pregnant.
Carl Morrissey, a very recent abductee, returns home to his wife. On being mugged, he discovers his power: to fight. So he decides to clean up the local park. Then he gets stabbed, and dies. But the neighbourhood carries on his work. Diana discovers there are microscopic gravitational anomalies at the place where each person was abducted. Shawn realises he can heal; Kyle has a relapse. Lily and Richard move in together; Lily says she can hear her baby's thoughts. Maia asks Diana if she can stay with her.
A serial killer starts killing again after a lapse of 23 years -- suspicion immediately falls on one of the returned, a suspect in the original killings, who dissappeared 23 years ago. But then someone else confesses, to all the crimes. Shawn revives Kyle. A talk-show host starts denouncing the 4400.
The brothers of one of the serial killer victims start bombing 4400 returnees. This seems to be part of the "rippple effect", as it makes the 4400 into sympathetic victims.
The reason for the returns is revealed -- it's an attempt by a future dying humainity to change their past