Grad school buddies Jay, Tyler and Will set out for a road trip after spending most of their last two years together. However, their relationships are tested when Jay and Tyler become the prime suspects in a terrorist bombing in New York City. After looking into the incident more, Jay and Tyler learn that Will may not have been the person they thought he was.
After being framed for a terrorist attack and fleeing New York, Jay Burchell and Tyler Fog are now on the run from the FBI. They escape to Carlton Fog's private retreat, but begin to question the loyalty of a power broker whom Fog has hired to save them. Meanwhile, FBI agents question Kim Doherty, Jay's girlfriend.
Tyler and Jay return to New Haven to retrieve items that may exonerate them from the terrorist bombing and implicate Will Traveler instead. Meanwhile, Carlton Fog issues a press conference regarding his involvement in hiding his son, and Kim's daily life begins to crumble as she searches for proof of the ever elusive Will.
Jay and Tyler take their search for Will Traveler to Will's hometown, Deer Harbor, Maine, while the FBI finds new evidence on the bombing in New York. In Maine, the guys meet a woman who planned to escape with Will after the bombing, and their search becomes deadly when Jay and Tyler uncover more of Will's associates.
Jay and Tyler's search leads them to Boston where a security box is uncovered containing aliases Will used and evidence about the bombing. After being captured by his bosses, Will Traveler undergoes interrogation and reveals what happened on the day of the Drexler bombing. A key arrest made by the FBI shows that the Drexler conspiracy goes far beyond what they had initially imagined.
Tyler and Jay risk a return to New York in order to investigate possible financial ties to the bombing. While Will Traveler seeks to avenge his girlfriend's death and bring down the organization, the FBI discovers that one of their own might be involved in the conspiracy.
Jay and Kim reunite for the first time since the bombing, while Will Traveler hunts down Maya's hugger in New York. Meanwhile, Tyler discovers FBI ties to the bombing and has to stop Jay and Kim from taking evidence to Agent Marlow.
Will Traveler's past is revealed when he reunites with Jay and Tyler to bring down Jack Freed, the man behind the Drexler bombing. Meanwhile, Marlow is suddenly taken off the case.