In the season opener it's months after the ability creating drug, Promicin, has been made available to the public. The side effect is that it kills half the people who take it.
Healer Shawn Farrel, who was put in a coma by the evil Isabelle, awakens with the help of his cousin, Kyle Baldwin. His father, NTAC agent Tom Baldwin, is steel reeling from the loss of the love of his life, Alana, who mysteriously disappeared in a flash of light. In a later episode we find out she was transported back into the past by the "future people". Tom's partner, Diana, returns to Seattle after spending half a year in Italy with her daughter Maya and fiance. She has learned that her wayward sister, April (Natasha Gregson Wagner of MODERN VAMPIRES) had taken Promicin and wants to know if she's dead or alive.
Meanwhile, there's a new head of NTAC, Meghan Doyle. She and Tom have an immediate attraction and become a couple. However, Tom starts acting weird, as if he's possessed. He is--by one of "The Marked". These are people from the future who want to prevent the 4400 from having any influence and changing the future. They want the cataclysm to happen so that their particular society will survive. They were able download their personalities into nano-bots which take over a host. Meghan and DIana realize what's happening but how do they save Tom? Is it even possible to save him?
Jordan Collier rises to power with the help of Kyle. Kyle's ability manifest itself in a weird way--he's able to know when things will happen and "know what to do" with the help of a young woman only he can see. She's a part of his mind. She urges him to become Jordan's "shaman", to urge him to do the right thing for their people. These plans are interrupted when the Marked eventually capture Jordan Collier. They want to possess him as well so he can undo all the damage he's done. Jordan's power is being able to remove people's abilities and they want him to do this with all the "infected".
In the last, and best episode of the season, THE GREAT LEAP, Shawn Farrel's brother, Danny, decides to take the Promicin drug and develops the ability to spread it, airborne. He infects thousands of people and nine thousand new people with abilities are created. The season ends with the P-Positives taking over all of Seattle. Even members of NTAC have powers. Meghan Doyle can turn anything into vegetation and analyst Marco and now teleport.
What happens next is covered in the recommended two books, WELCOME TO PROMISE CITY and PROMISES BROKEN.