On the train to Deer Harbor, Jay is struggling to stay awake. He notices that the passenger next to him is reading a newspaper with his picture on the front and turns around to face Tyler, who's sitting behind him. Tyler motions, very casually, over to a young boy sitting in the next aisle. The boy hasn't taken his eyes off of either one of them since they got on the train. Jay tips his head towards the exit, and both he and Tyler head toward the end of the car.
About halfway up the aisle, one of the other passengers recognizes them as the Drexler suspects, and chaos ensues as the rest of the train tries to capture them. Tyler, panicked, calls out for ideas on how to escape, and Jay tells him to pull the emergency cord. He tries, but is herded into a nearby seat and held by four passengers. Jay manages to overpower his assailants and manages to reach the cord, but a federal marshal warns him to halt. Jay pulls the cord, the train stops suddenly, and in the interim the marshal's gun goes off, striking Jay in the shoulder. Just then, Jay hears Kim's voice calling out, and she appears next to him. Suddenly, Jay is snapped awake and back to reality when Tyler tosses his bag roughly into his lap. Startled, Jay looks around at the half-empty train car, where the passengers are either asleep or unconcerned about them. Tyler whispers sternly that "it's time to go," and the two make their way toward the end of the car without incident.
It's been forty-four hours since the Drexler bombing, and Jay and Tyler have made their way to Deer Harbor, Maine - the supposed hometown of Will Traveler. As the train leaves, Tyler asks Jay if he managed to get any sleep. "Not enough," he replies, and Tyler concurs: he's only managed to get about five hours in the last two days himself. "If we don't get some sleep soon, we're not going to be on the run for very long," he muses soberly.
Jay takes the train schedule they found in New Haven to the train station, determined to figure out what the handwritten code is on the bottom. The ticket agent explains that it's a reservation code, but won't give them the name it was placed under until Tyler manages to convince him with a very nice tip. The ticket was for a "Daniel Taft," a name they've never heard before…unless "Daniel Taft" was an alias that Will was using. The two head into town, convinced they can find someone who might have known Will, but as they walk down the street Tyler becomes convinced that they're being followed. Jay tries to pass this off as paranoia, but Tyler's not as assured; after all, they're not even sure who they're looking for at this point! When Tyler tells him he wants to leave, Jay tells him that that might be a bad idea, and points him towards a sign on a small bookshop: Have Books, Will Travel. Jay goes into the bookshop, convincing Tyler that to go in together all the time is bound to attract attention, and questions the shop's owner, Maya. He buys a copy of On The Road, but if there's anything Maya knows, she's doing a great job of not telling them. Meanwhile, two men are listening in on the conversation through hidden transmitters.
In Manhattan, Agents Marlow and Borjes are sifting through what they salvaged from Nell's home in New Haven. Among the articles they found untouched are a manifesto supposedly written by Jay and a video that's being broadcast over the internet featuring Tyler railing about the government. Though the editing of the tape is bad at best, it remains a link between the boys and the bombing. Marlow, still not completely convinced of the boys's guilt, questions the authenticity of the tape, but Borjes lays it out for her: the prints match, the fibers match, and they even gave the boys the chance to come in "and they still ran."
Elsewhere, Kim is sitting in lockup after her assault of the photographer behind her apartment. The guard comes and tells her she's in luck- the photographer has decided not to press charges. Skeptical, she looks out into the hallway and sees Agent Chambers standing there, waiting for her.
In Deer Harbor, Jay and Tyler sit in a coffee shop discussing the mysterious Maya. Tyler, convinced that she's hiding something from them, wants to go back and confront her. "And do what -say 'please'?" Jay quips. He tells Tyler to give him a minute to think, but Tyler, feeling left out of the planning process, asks Jay when "this became a one-man show." Jay tells him that following her might not lead anywhere, and following her advice to go to city hall will only get them arrested by the police force based there. "If you're going to make suggestions, make good ones," he says in mild exasperation.
Tyler steps out to a nearby phone booth for a moment, and as he does Jay looks over at the television and catches snippets of the video the FBI has been analyzing. His mind wanders back to a point six months ago when he, Tyler, and Will were watching a press conference that President Shears was giving about a "working vacation." Will and Tyler both heckled the speech, but Jay wanted to listen in and told them to keep it down. Will then brought out his video camera and began asking the boys about their thoughts on the President and his actions in office. Jay begged off, but Tyler was more than happy to give his two cents. He said then that the President had "sold this county to the highest bidder" and that it was time for the people to rise up in revolution. Though the message was unsettling, Tyler's tone of voice clearly said that he was merely blowing off steam and didn't mean what he was saying. However, in the present, that message has taken on a whole new connotation ...
... and it's one Jay shares with Tyler in the back of the men's room. He tells Tyler about Will's video being all over the news, and his quote about "blood in the streets" being quite prominent. Tyler tells him that he was kidding then, and Jay tells him that the video was part of the frame job against them. Infuriated, Tyler asks what they should do now, and Jay tells him that in all honesty he'd like to just find Kim and disappear, but "since that's not an option, I guess we keep looking for Daniel Taft." Tyler tells him that he was able to track a listing for Daniel Taft, but it wasn't one for a house.
In Manhattan, Marlow and Borjes are trying to get both the originating IP from Tyler's video and examine the handwriting on Jay's manifesto. In the latter case, Marlow tells Borjes that though the handwriting is similar, "the P's don't match up." She then goes into an interview room to talk with Jay's mother, who has a Christmas card from her son dated 2002 - the last time the two of them talked. Though she's wary about trying to incriminate her son, Marlow asks Jay's mother about why it is they don't talk. She explains that he believed they were abandoning his father in his time of need, while she saw it as protecting her son. When Marlow asks whether Jay could do something like this, his mother replies that there were times she questioned the goodness of her husband - but never her son.
Jay and Tyler head for the docks in Deer Harbor, looking for the boat slip Daniel Taft owns. They find it, but there's no boat to be found. Looking around, they see a boat in dry dock named the Maya - the name of the woman from the bookshop. They head inside the boat, while unbeknownst to them a familiar face watches.
Agent Chambers drives Kim home, leading her through the media circus and taking her up to her apartment. She reminds him that his people have already searched her apartment, and he suggests that she should leave town for a while - perhaps a visit to her parents. Kim tells Chambers that she'll be fine, but Chambers tells her that he too has a daughter about her age and though he lets her live her life, he's not afraid to step in when things go badly for her. He also tells her that though she doesn't want to hear it, the simplest explanation is usually correct: in this case, that her boyfriend and his friend committed the bombing on the Drexler as opposed to a massive conspiracy that's been underway for the past two years. Kim thanks him for the concern, but sends him on his way. In the car, Chambers says to an unseen person that "Ms. Dougherty is gonna help our case."
Inside the Maya, the boys begin turning the place upside down looking for evidence of Will. Jay manages to find a box full of handguns; Tyler finds a stash of MRE's. Whoever Will is, he obviously planned to be gone for a long time. Tyler sets upon the idea of finding out whether Will charted a course until Jay hushes him- there's someone coming inside! With no place to go, the two look on and wait for the person to show themselves. A man enters, and asks what they're doing on his boat. The two apologize, saying that they're looking for a friend, and Tyler asks the man if he is Daniel Taft. The man says he is, and that this is his boat.
At FBI headquarters, Marlow and Borjes are discussing the chemical compounds from the Drexler and the New Haven boxes. The chemist tells them that the compositions match each other, but he has some doubts. When Marlow tells him to spill, he explains that napalm is only kept in small quantities at two specific military bases, and that neither has any missing. He also explains that though one of the boys has had some chemical engineering experience, a compound like napalm can't be made by someone with rudimentary experience. Usually, he says, people use 40 pounds of fertilizer and blasting caps to get their point across, not something as sophisticated as napalm made from scratch. Though it's not impossible that the boys blew up the building with this compound, the chemist says that it's extremely unlikely that two grad students could come up with the substance from scratch, no matter where they went to school.
Marlow reports to Chambers about her findings, and he asks her about her thoughts. She replies that the boys are creating a profile like nothing she's ever seen - though evidence says one thing, their personalities and character witnesses say something completely different. Though there are questions about Jay's handwriting in the manifesto, and the chemist's findings of homemade napalm that's extremely sophisticated for grad students, Chambers states that evidence still places Jay and Tyler at the top of the list. Marlow tells him that after speaking to his mother, she realizes that Jay's father literally died proclaiming his innocence, even after losing everything he held dear. When Chambers asks if she thinks Jay might do the same, she replies in exasperation that "he won't stop running."
On the boat, Jay and Tyler question Daniel Taft about Will. They explain their "mix-up" and begin to ask questions about where he's been for the past couple weeks. Taft says that the boys must have been pretty close to this "friend" of theirs if they knew he wouldn't mind them going through his things, and states that Will must have been from elsewhere, as in a town as small as Deer Harbor he'd have heard of him, but he hasn't. Tyler queries about the stash of guns and supplies, and Taft explains that it's a habit from his days in the Marine Corps. A quick look at a marking on his hand tells Jay that the man was 1st recon - same as his father was.
Jay's mind flashes back to the day of the presidential speech, when Will began asking Jay about his thoughts on what happened to his father. Though Tyler chided him for being a jerk, Will was insistent: what if Jay's father was blamed to save some higher-up from losing a star? Jay pondered this, but Will noted that everyone, at some point, lies.
Finally, Taft excuses himself to make a phone call, and tells the boys they're welcome to stay for a beer if they promise not to go through his things anymore. The boys make their apologies and Taft leaves, locking the hatch behind him. Both Jay and Tyler realize real quick that Taft is not who he says he is, and make to leave, until they notice the locked door. After trying to call out for Taft to unlock it, Tyler sees him hop in the car and take off. Jay then picks up one of the handguns and fires at the door, startling Tyler in the process. He manages to shoot off the lock, then drops the gun and both of them scramble out the hatch to find a nasty surprise - a bomb that's about to explode! The two manage to dive off of the craft before it explodes into flames. Under watchful eyes, the boys manage to convince Taft that they died in the explosion, and then take off.
In an FBI briefing room, Chambers gives an "update" on the case. Marlow is infuriated, mainly because Chambers used parts of what they have and presented them as fact to the press. She tells him that misleading the press can not only hurt her investigation but creates unnecessary fear. Chambers warns her that "repeating her mistakes" from an earlier case in Trenton where an agent was killed is not in her best interest. Marlow counters, saying that she's not the only one who shares her stance, and they both look at Borjes, who shrugs.
In Deer Harbor, Maya is getting things in order around her bookshop; she's packing a few things and making preparations to leave when Jay and Tyler burst in. Tyler, furious about the lies and nearly being blown up, begins railing on the woman until she angrily motions them both outside. She tells them that people listen in inside the bookshop, and that she can tell them more later if they follow her. Jay balks, pointing out that she's already lied once, and how do they know that she isn't lying now? Maya rattles off three pieces of information: Jay's whole name, his score on his LSAT's, and the name of his favorite baseball team (the Chicago Cubs). Convinced, the boys follow her.
In a building across the street from the bookshop, Taft enters a room to find that his partner is dead and the equipment is destroyed. When he realizes there's another person in the room, he begins to tell him what kind of mistake he's making ... until he sees that it's the porter from New York. The Porter demands to know what they know about Will Traveler, and Taft tells him they know nothing - they just were supposed to monitor the bookshop. He also tells the Porter that "you're not the only one after him," and that he doesn't know anything about Traveler. "You lie," proclaims the Porter, who promptly shoots Taft where he stands.
In Washington, the agent at Homeland Security begins typing in a password on his computer. He gains access to satellite maps of Deer Harbor, and calls some associates of his, asking them what their location is. The associates tell him that they are within minutes of Deer Harbor, and they make steady tracks for the bookshop. Maya, meanwhile, ushers the boys hastily inside her house. She then asks about the man calling himself "Daniel Taft," and Tyler reiterates that he said the boat was his and then tried to blow the two of them up in it. To their surprise, Maya tells them that the man they met was not Daniel Taft - because that was the name Will used when she first met him. She says that the boat was supposed to be their "out," and that she recognized the boys from videos Will has shown her. When Jay asks why she lied, Maya tells him that she had hoped "you'd just go away ... for both our sakes." Tyler, trying to keep his fury to a simmer, states that she's obviously a terrorist along with Will and whoever else is after them and turns to leave.
Maya stops him, declaring that neither she nor Will were terrorists. Five years earlier, her brother was caught on drug trafficking charges, and she got brought up on charges because the brother used her store as a stash point. Then a lawyer came to her, saying that he could make the charges disappear if she went to work for his bosses. "I wasn't in a position to refuse," she says.
The associates of the agent arrive at the bookshop, and break in to find what they're looking for to be missing. The Porter watches as a white van makes tracks for an unknown location, and he follows it.
Maya tells the boys that when she met Will, she met a man who truly believed he was serving his country by working for his bosses. He came to her a few years ago, hoping to build his cover about being from the area when he went undercover as a student. Jay asks her when she last spoke to him, and she tells him it was two weeks ago. She relates the incident, when Will seemed spooked and was told that the order had come in. He told her that he'd finish the job, and then they'd get on the boat and not look back. When she asked what to do if he didn't return, he told her to take the boat and go without him. She says that afterward, all of her attempts to contact him have come up empty, and Jay says that he died in the bombing. "I wouldn't be talking to you otherwise," she says crisply.
As the associates of the agent make tracks from the bookshop, Mays tells the boys that despite what they might think, Will liked them. She recounts the way he talked about them, and that Will couldn't understand the friendship between "the rich kid and the soldier's son." Tyler comments that setting them up for a terrorist attack is some way to show friendship, and Maya counters that he was following orders. She then receives a phone call and tells the boys to leave, and fast - there are people coming that are looking for them.
Before they leave, Maya says that she's tired of being used by these people, and that she's leaving as well. She gives them an old skeleton key that Will gave her for safekeeping, telling them that whatever it unlocks would reveal evidence - perhaps it will help them now. She shoves them out the door just as the agent's associates burst in. One of the associates calls, saying that they missed the boys, but they have the girl - and Traveler is nowhere to be found. The agent states that he has others working on those angles, and that they should come in.
In Kim's apartment, her father complains about the media circus outside. She states that her neighbors don't speak to her anymore, and he complains about the actions of the press and about hounding innocent people. While she thanks him for the sentiment, he makes it clear he only means her, not her boyfriend. Kim, who's not in the mood to argue, just finishes packing some things and her father takes them down to the car. Her face is filled with doubt and worry about Jay and the whole situation.
Meanwhile, Tyler manages to "borrow" a cell phone - for a price. He hands it to Jay, who's nervous about making a call. Tyler tells him that he's wanted to make this particular call all day, and that if the FBI traces it, so much the better - maybe they can find something the two of them overlooked.
Jay takes the phone and calls Kim, who's relieved to hear him. She asks him why he's still running, and he tells her that it's complicated. She then asks what happened with the man upstate, and he explains that neither he nor Tyler killed him - in fact, the man was trying to kill them. Kim tells Jay she wants to help them, but she doesn't know anything that can help and then there are the reports on all the dead bodies that seem to follow them. Jay tells her that what she hears is not the truth, and that no matter what happens, she'll be okay. Just then, her father takes the phone from her and tells Jay, "You don't think this phone is tapped?" before hanging up. Worried, Jay returns the phone and says that Kim's father was with her. Tyler remembers that the two don't get along, and Jay says that's what's got him worried. Tyler tries to reassure him, but Jay focuses on the approaching train. Tyler, however, becomes convinced that he sees his car parked in the station parking lot. When Jay tells him that the color is wrong, Tyler adamantly tells him that the grill is broken in the exact same way as his was. Jay blames the confusion on lack of sleep, and Tyler resignedly agrees.
Jay, however, gets a nasty surprise of his own - he sees a form he recognizes all too well get out of the car. "It's Will!" he tells Tyler, and he begins to shout over to him. Will, who realizes who the voice belongs to, does not look at all happy to see them, and before Jay and Tyler can approach the passing train speeds through, right between them, making it impossible for them to catch Will.
Will, meanwhile, has other problems - the Porter has found him, along with his bosses' associates. The Porter shoots at Will, telling him to stay down, but Will runs and is easily captured by his bosses' men. As they drive off, the train clears and Jay and Tyler are left with a car, no Will, and the sight of the Porter, who they remember from New York.