Under the leadership of a new director, Meghan Doyle, NTAC faces off against a high school student named Graham Holt who developed the ability to make people worship him like a god.
Tom and Diana race to find the person behind an ability that makes people's phobias come to life. Meanwhile, Kyle's mysterious new friend, Cassie, leads him to a book that contains a prophecy about Jordan Collier. Shawn's brother, Danny, tells Shawn he wants to take Promicin and asks for his help in obtaining a shot.
Audrey Parker, an elderly woman, takes Promicin and develops the ability to astral project. No one can see Audrey's projection, which allows her to look in on other people's lives and share their most intimate moments.
Diana locates her sister, April, who took Promicin and developed an ability that puts her life in jeopardy. Meanwhile, Shawn is approached to run for public office and Kyle keeps Isabelle safe while on the run.
Tom follows Kyle to a small town populated by Jordan Collier and his followers. Kyle has come to show Jordan a book that contains prophecies about the future. Now Tom must fight to stop his son from joining Collier's movement. Meanwhile, Maia deals with a very disturbing vision of the future.
Tom and Diana search for Curtis Peck, one of the 4400 who makes movies about the theories he has. Meanwhile, Jordan tries to get Shawn to rejoin the movement.
Jordan Collier's movement takes a huge step forward when his followers settle in the heart of Seattle. Diana panics when Maia turns up missing and Shawn runs into some trouble, in the form of a woman, in his bid for public office.
Tom, Diana, Jordan, Shawn, Kyle, Isabelle, Maia, Meghan, Marco, PJ and Brady all wake up inside NTAC without any memory of how they got there. Trapped inside the building, the group must put aside their differences and work together to find a way out. Meanwhile, Tom and Jordan Collier must work together to save the life of a mutual loved one.
Richard surprises Isabelle when he shows up in Promise City but the happy reunion takes a turn when Richard kidnaps her hoping to start a new life with his daughter. Meanwhile, Tess, her schizophrenia out of control, uses her ability to take control of people at a diner, forcing Kevin to call Shawn for help.
The Director of National Intelligence pressures NTAC to pursue Richard and Isabelle Tyler. Richard is visited by his dead wife. Meanwhile, Shawn and Kevin Burkoff announce that they have developed a test that can tell people if taking Promicin will cause their death. Tom dreams about the future and the 4400.
A computer virus attacks a large software company owned by a suspected member of the Marked. Elsewhere, Maia visits Promise City and receives an unexpected birthday gift.
Isabelle works with Tom in order to get close to Jordan. Rebecca Parrish talks to Tom about the Isabelle plan, concerned that Maia's visions could complicate things if she had the wrong vision at the wrong time. In Promise City, Tess get a few citizens, including Shawn, under her power in order to get Kevin out of confinement. Tom and Diana face off.
As paramedics try to resuscitate Susan Farrell, they say that they believe she took Promicin and lost the 50/50 lotto that comes with it. But Danny is certain she did not take the shot. After arriving at the hospital with the paramedics, everyone around Danny starts to die. Garrity and another NTAC agent are sent to the hospital to assess the situation. Seattle falls into chaos and the NTAC must look to Promise City for help.