Tom and Alana tell Kyle about the alternate reality and that they're now in love, and he accepts it. However, when he finds out that he went to Stanford, he is afraid that Tom isn't proud of him.
Meanwhile, Jean DeLynn Baker (disappeared October 27, 1999) finds herself alone in a town whose citizen's are all dead.
At the 4400 Center, Shawn is having trouble managing the place, so Matthew Ross, who was told by Jordan to help Shawn in the event of his death, comes to help.
Elsewhere, as April uses Maia's powers to pick winning scratch tickets, Tom and Diana are taken off of the Collier case and are sent to Granite Pass, Oregon, where an outbreak of a lethal virus occurred. The only survivor is Jean Baker, a returnee. As they later arrive at the town and find that the virus had dissipated half an hour after it was released, Jean hitches a ride with a truck driver and heads to the 4400 Center. She stops at a motel and calls the Center and tells them what happened. Ross finds out and called NTAC. Back at Diana's apartment, Maia helps April with gambling and doubts that she loves her for who she is, so April takes her out for pizza.
On the way to the motel, Tom and Diana find the trucker dead. NTAC breaks into the motel and ties to take Jean. However, she gets scared and releases the virus, which gets through their hazmat suits! She then steals one of the agents' cars and calls Tom, saying she is going to kill herself. As Tom and Diana follow after her, Tom calls Marco, who explains that the virus coincides with her blood flow. If she gets angry, confused, or upset, the virus will be released.
Meanwhile, Shawn decides to leave the Center for a few months, but Lily, who was made Assistant Director of Human Resources by Ross, convinces him to instead set up a foundation and heal one person a day. Also, April bets her mother's engagement, but Maia lied to her about who would win the game in order to see if April truly loves her.
Jean's car is found on fire, and everyone thinks that she is dead. However, she calls Tom and reveals that she now believes that the Book of Revelation is about her. Tom and Diana track her down to Portland, where she is about to willingly release the virus. Tom manages to talk her out of it, but since she can't stop it, Diana shoots and kills her.
Later, Marco gives Diana a fake diary, and she gives it to Jarvis. Meanwhile, Ross thanks Lily for convincing Shawn into creating the foundation. She then tells him that she's not a believer of the Center, and he reveals that he isn't either.
As Kyle watches a news report about Collier's death, he begins remembering the shooting. Elsewhere, a man who saw Kyle enter the building from which he shot Jordan helps in a sketch drawing of Kyle. The picture is then passed out throughout the NTAC building.