When Wallace gets kicked off the basketball team for failing his drug test, Veronica starts up with her old hobby: investigating. She successfully solves the case her first time back on the job, uncovering a plot by several wealthy parents to get their children starting positions by rigging false positive drug tests for the competition. While doing so, Veronica looks back on how her relationship with Logan fell apart over the summer. The same night Aaron Echolls was arrested, Logan was jumped by Weevil and the rest of the PCH gang who believed that he was Lily's killer. After being knocked out, Logan wakes up next to the dead body of PCH biker Felix with a knife in his hand. Logan is accused of the murder, but he is quickly dismissed of the charges. Because of his continued self-destructive behavior, Veronica breaks up with him. She and Duncan don't officially get back together till Veronica's eighteenth birthday, where Duncan gives her a fortune cookie with a message inside. She also tries to deal with the new hatred between her and former friend Meg, who was dumped by Duncan on the last day of school.
In the end, Veronica goes on a school field trip with a large number of classmates and during a rest stop, is distracted by the ghost of Lilly. As a result, Veronica is left behind while she and Weevil verbally spar over Veronica's decision to attempt to return to her old life as a member of the 09er clique at school, and her belief that Logan was innocent. However, Veronica soon finds out being left behind was a good thing when she and Weevil (who decides to give Veronica a ride home) discover that the bus containing Meg and a half-dozen of Veronica's classmates has crashed off the cliff and into the ocean.
On the bridge after "Leave It to Beaver", Logan was beaten up by the PCH bikers. When he woke up, Felix was dead beside him and Logan was holding a bloody knife. He threw the knife in the water and went to Veronica.
Deputy Leo came to Veronica's to arrest Logan. There was a long investigation, during which Veronica supported Logan, and eventually the charges against Logan were dropped because of a lack of evidence.
A civil war escalates in Neptune, with Logan and Dick burning the community pool.
It's shown that last summer, Veronica broke up with Logan because he was recklessly destroying the town and seemed to be having fun.
She begins going out with Duncan, who is now Logan's enemy.
Near the beginning of the episode, Veronica says, "Logan and Duncan don't speak anymore. I guess that's what happens when your best friend starts dating your ex." The audience is led to believe that she's going out with Logan and not Duncan. But it's later revealed to be the other way around—that Veronica broke up with Logan last summer, and started dating Duncan.