Veronica debates coming clean to Nicole. Veronica’s fidelity is tested. Veronica and Keith discover they aren’t the only ones who believe they’ve found the bomber; a surprising potential client to hire Mars Investigations.
Veronica Mars and Keith Mars have their suspicions about Big Dick committing the first two bombings (Sea Sprite and Perry Walsh), and Penn Epner, the pizza guy, being a copy-cat bomber who set off the last three bombs. Their theory is all based around a nail - which Penn and the Murderheads thought was some shrapnel from the first bomb. Really, the nail came from a piece of art in the hotel that got ripped apart. They think that the second bomber assumed the nail was from the first bomb and then created bombs from these nails to imitate the initial bomber.
The Mars approach the Chief of Police about it and she agrees to put out an ABP for Penn to find him. They raid his apartment and find printed materials about how to create bombs. Penn is nowhere to be seen, and was last seen leaving with a packed bag (they assume to his girlfriend's cabin).
Big Dick offers Matty Ross a bribery car, in hopes that she will sell the Sea Sprite and stop looking for answers about who the bomber is. This offer makes Matty even more sure that Big Dick is the bomber.
Veronica and Keith track down Penn to a remote cabin. Dodie Mendoza and Alonzo Lozano follow her there, in hopes that they can kill the bomber AND the Mars (knowing that they suspect them). Veronica and Keith tell Penn that the gig is up and he is caught. Then, Dodie and Alonzo start shooting at all of them. They get into the house and try to protect themselves, but they almost ran out of bullets.
Fortunately, Weevil and his gang, hearing that Alonzo threatened Veronica, come to the rescue. They tell Alonzo and Dodie to back off. The Mars and Penn walk away alive - Penn then gets arrested. Veronica and Keith are awarded the $250,000 reward that was offered.
Leo D'Amato leaves to go back to Virginia since the case is now closed, as Penn was caught. He says bye to Veronica and leaves on friendly terms.
A new letter was sent by the bomber, saying that there will be another bombing later that week at noon. The letter is written with a limerick. Everyone asks Penn if he knows where it is, but he maintains his innocence.
Keith announces that he will retire from Mars Investigations because he is losing his memory and almost got himself and Veronica killed (because he forgot extra bullets when they needed them in the shootout). Veronica is upset by this idea but Keith tells her he has no choice.
Logan Echolls surprises Veronica by coming home. She immediately asks if he still has the ring because she wants to accept his proposal since she had a "moment of clarity" from her near death experience.
In a surprise twist, none other than Penn calls Veronica and Keith asking to hire them. He claims he is NOT the bomber and that he wants them to prove his innocence. Hesitantly, they agree, having doubts that maybe they were wrong in accusing Penn after all. They start to look into it.
Big Dick and Clyde Pickett have some differences, since Clyde was promised a beachfront property for his help in the bombing and Big Dick says it "escaped his mind" and he sold it to someone else. Clyde is upset, and realizing (after Keith gave him a heads up) that if Big Dick is arrested in connection with the first bombing that he will give up Clyde and he will go back to jail.
Clyde decides to approach the Mexican cartel guys to offer them a "gift". The gift is a recording of Big Dick admitting his involvement in the bombing. Alonzo and Dodie are happy to finally have the bomber they've been looking for. Clyde is happy because he knows that they will kill him, and his connection to the bombing will be eliminated.