Okay. A lot happened, and I'm writing this from memory of only one viewing, so forgive me if I miss anything.
Tyler and Jay are on a train to Maine. They get there and ask the man at the station about the number Will had written on his train schedule. The man tells him that it's a reservation number, and after Tyler greases his palm, the guy tells them that the man that made the reservation's name was Daniel Taft. Who is this Daniel Taft, they wonder? Is Will using that name? Or is Daniel using the name Will?
They are considering this when they spot a bookstore named "Have Books Will Travel." So that's where Will got his name, they think (duh), and Jay goes to the store to ask the pretty girl that works there (Maya) about it. She gets all shifty eyed and suspicious and shuts him down when he questions her, and we see that the store is bugged and there are men listening to the goings on there. Jay tells Tyler he didn't find anything out, but Tyler called information (handy idea) and found a listing for Daniel Taft.
They go the address, which is a slip at the marina. There is no boat in the spot marked "Daniel Taft," but they see a boat named "Maya" and decide to check it out. They find a crapload of guns and stuff. At this point, we see the Hotel Bellhop from Episode One is watching them. We also see another man climbing aboard the boat, and it's not Will. It's just a random guy. They ask if he's Daniel Taft and he says yes, but I didn't believe it. They are so trusting! They're also not subtle or sneaky at all. Anyway, they tell him they were looking for their buddy Will Traveler and he says he doesn't know Will. He tells them to help themselves to beer and that he'll be right back. He slaps a bomb on the boat and locks them in. Jay grabs a gun to shoot them out, and they narrowly escape (again).
A video appears on the news of Tyler talking trash about the President, and Jay remembers Will taping it, egging him on, and smirking. The FBI folks are using this as "further evidence" of the guys' hatred of the administration. The FBI lady (Marlow) wonders why the guys would go to Nell's to try to destroy the video if it was already online and in the open. She's thinking that something's amiss, but she can't get her fellow agents to go along, because they just want to close the case.
Meanwhile, Jay's girlfriend Kim is in jail for punching the photographer, but is released when FBI big boss comes to pick her up. I can't decide if he's truly BAD or if he's just blinded by the desire to solve this thing. He tells her, fatherly-ish, she should go stay with family until this is over.
So. They go BACK to the bookstore to press Maya for answers. She tells them to shut it and takes them outside and tells them "they're listening." She takes them to her home and gives them some story about how Will is Daniel Taft, how he told her about them, how he thought he was serving his country, how she and Will were going to run away together after the mission. Bellhop guy is watching as the Listening Men come careening into the store, then drive away. Maya gets a call that the Listening Men are on the way. She gives Jay and Tyler an old-fashioned skeleton key, says that Will didn't tell her what it was for, only that if they needed to, they could use it to fight back. She sends them away and tells them she'll be fine, even as the Listening Men are breaking down the door.
The guys are at the train station, and Jay calls Kim. She cries and they talk, then her Dad gets on the phone and tells Jay to leave her alone. This worries Jay because Kim and her dad don't get along. What worries Tyler, though, is that he sees his car parked in the train station parking lot. His car, the one he left in NYC before the bombing. Jay's like, "no way," because the car is a different color, plus, that's nuts, but Tyler is sure. Then we see someone get out of the car, and it's WILL. Jay screams to him, but just then a train passes by and Jay and Tyler can't see any of what's happening on the other side.
What's happening on the other side is: Will's going to bolt, but a white van comes screeching up, Bellhop shoots at the van, but they snatch Will up and drive away, Bellhop shooting all the while. The train passes, and the guys see Tyler's car still there, but no Will. Then they see Bellhop, and Bellhop sees them. They are wigging right out, and rightfully so.