Three months have passed since the events of "Fifty-Fifty". Tom is still searching for Alana. Jordan, Tess and Kevin are still in hiding. Shawn remains in a coma following his encounter with Isabelle. Diana, Maia and Ben are in Spain. Isabelle is in NTAC's custody. Promicin is still getting to the public, despite laws forbidding its use. NTAC has a new director, Meghan Doyle. In addition, Richard, who was last seen walking away from the 4400 Center, has gone missing, and Kyle has returned home.
Jordan has been having strange dreams about the future, thinking he has stopped the catastrophe, but hating the fact that sacrifices had to be made. Tess has started to hallucinate about people dying, feeling guilt over the deaths that promicin has caused. Kevin informs Jordan that if he has to choose between helping him and helping Tess, Kevin will help Tess. He also tells Jordan that Tess will soon need more medical help and can not remain in hiding. Eventually, Tess leaves Jordan's hideaway.
Diana has decided to take a job as an adviser regarding the 4400 in Europe; Ben and Maia support her decision. But Marco calls her to inform her that her sister, April, may have taken some promicin. Diana, worried that she has not heard from April for several weeks, leaves for America. Maia and Ben remain in Spain, but Maia predicts that Diana will not be returning.
Kyle is ready to do anything to wake Shawn up, returning the favor, but the promicin Kyle took is having no effect on him. Kyle meets a girl in the park named Cassie, whom he befriends. She knows who he is because she has read a lot about the 4400. She suggests that a shot of promicin might "jump start" Shawn's system, because it is inside him already. Kyle tells her he already thought of it and that the doctors will not consider it, but that they also say that Shawn should be awake since his brain is working and his vitals are good.
Tom goes to see Isabelle, who asks if Shawn is all right. Tom tells her and asks if she knows where Alana is. Isabelle does not tell him what she knows because she does not want to ruin his hope, but she reminds him that the people from the future told him to kill Isabelle. Because he did not, they could be punishing Tom.
Meanwhile, a teenager named Graham Holt has started to develop 4400 powers from the promicin he took. Graham is seen as a messiah and people begin to do whatever he tells them. People start to dress, worship, and offer themselves to him. Soon Graham has taken over his entire high school; the principal calls NTAC. Tom and his team get there, but Graham's followers prevent Graham from being taken back to NTAC. Tom calls in the army, but Graham has taken over a section of Seattle with his followers, who prevent the army from getting to him. Tom leaves after he offers Graham time to come out. Graham is able to take the army, police, and most people in Seattle under his control.
When Tom returns to his home he finds that all of television channels are either off the air or broadcasting Graham's image. When Tom arrives at the NTAC parking garage, he discovers the police (under orders of Graham) arresting everyone. Tom grabs Meghan and they both go back to Tom's house to think of a way to stop Graham.
Jordan sees the Graham broadcasts on television, hating that promicin was used for it. Kevin notices Tess is gone and goes looking for her as Jordan goes after Graham. Jordan allows himself to be captured and is taken to Graham. Graham tries to convert him, but to no avail. Jordan instead uses his ability to remove all the promicin from Graham, negating his control on the city.
Kyle injects Shawn with promicin and although he appears to go through a seizure, he soon regains consciousness. Relieved, Kyle searches for Cassie to tell her what happened. She is not enrolled at the college she claimed to attend, and he is unable to find her.
Back at NTAC, no promicin is discovered in Graham's blood. Meghan hands Tom a note from Isabelle, telling him to go to a museum and he will find what he is looking for. He finds a painting of Alana hanging there; it was painted in 1885.