As the end of the first year at Hearst College draws to an end, the election for sheriff in Neptune comes to a close and Veronica and Piz discuss the effect a summer apart will have on their relationship.
As the escape is in progress, Warden Pope and Captain Bellick begin a search to detain the escapees. Michael and company struggle to reach the airfield as the police is hot on their heels. Veronica discovers a major piece of evidence that could prove Lincoln's innocence. The Vice President is worried about losing her authority.
Mulder and Scully return to the town of their first X-Files investigation where a UFO has crashed in the forest. CSM arranges for Krycek to be released from prison in order for him to make contact with the aliens and begin rebuilding the 'Project', while Scully's health appears to be taking a turn.
Kakashi must act quickly to calm Naruto down before he releases too much of Kyubi's power. Meanwhile, Deidara is cornered by Gai's team, and when he realizes that he can't defeat them, he decides that the only way he'll die is he takes everyone else with him!
Col. Tigh attempts to decipher the strange music he is hearing in his head while Baltar's trial comes to a conclusion. Key members of the fleet discover that they may be the Final Five Cylons.
Roger begins to release photos of himself to the local media for extra cash, prompting the CIA to initiate an Alien Task Force. Through a twist of fate, Roger ends up in charge of the task force in disguise, creating tension at home as he is now Stan's boss. Meanwhile, Francine comes to grips with being left-handed and Roger frames Stan as an alien in attempt to keep his identity a secret. Guest star: Raven-Symone (Katie)
Jake and Hawkins have one chance to expose the conspiracy behind the September attacks and the Cheyenne cover up to the independent Texas administration. However, getting there proves to be the most difficult part of their plan.
Beck uses extraordinary measures to show Jake and the town of Jericho that he is in control of the town. Hawkins learns who the mastermind behind the September attacks is.
Jake and the Rangers take on Goetz and Ravenwood while a Jericho Ranger makes a choice that will alter his life. An old friend comes to warn Heather that her loyalties to Major Beck have placed her in serious danger.
Hawkins receives a call on from someone who knows who he is, where he is and lets Hawkins know exactly when he'll be caught. Meanwhile, tragedy strikes.
The deadly Hudson River virus hits the area and a vaccine is being withheld from the citizens by a government official. Jake and the Rangers find a way to protect Jericho.
Jericho gets ready for a very important visitor from the new Cheyenne government. Hawkins and Chavez work to find the new leaderships secrets.
Following the battle of New Bern, Jericho begins the rebuilding process, while the Cheyenne government shows a particular interest in the town. While the dispute between Jericho and New Bern is being sorted out by the Cheyenne government, Hawkins has an old friend come to Jericho.