When Duncan disappears with Meg's baby, Lamb must work with two FBI agents to extract as much information as possible from an uncooperative Veronica. Meanwhile, Wallace reveals the real reason he returned to Neptune, and Weevil and Logan make a breakthrough in their hunt for the rogue gang member.
Wallace's hopes of escaping his trouble in Chicago are dashed when Rashard's uncle accuses him in the press of a hit and run. Meanwhile, Weevil has Veronica bug a church confessional to smoke out the traitor in his biker gang, and Keith acquires the interrogation tapes from the bus crash investigation.
Someone steals the cash box with $12,000 at the school carnival. As accusations fly, Veronica, rather surprisingly, finds herself defending Jackie. Meanwhile, Beaver stands up to Dick, and Logan meets a bright girl named Hannah.
Neptune High's closeted gay teens turn to Veronica for help when a blackmailer cracks into a private Internet bulletin board and threatens to publicly out everyone associated with the site unless they pay $5,000 apiece. Meanwhile, Keith continues to work on a case for Terrance Cook while looking into bus crash leads. Also, Logan romantically pursues Hannah, much to her father's distress.
Wallace's new girlfriend Jane enlists Veronica's help when her older sister Heidi appears to be a "runaway bride," but the clues suggest something possibly more disturbing happened on the way to the altar. Meanwhile, Keith and Veronica decide that they have no choice but to go to Sheriff Lamb with the evidence they've uncovered about the bus crash. Later, Kendall has a tempting offer for Aaron Echolls.
While accompanying Wallace to Hearst College, Veronica runs into her ex-boyfriend Troy. The next day, Troy is accused of raping a girl on campus and then shaving her head, and Veronica reluctantly agrees to help him. Meanwhile, Keith helps Cliff with a personal problem involving a prostitute, and Logan makes a decision regarding his relationship with Hannah.
Weevil believes that Thumper killed Felix and he asks Veronica to help him prove it. While Logan wins an essay contest and gets to intern for a week with Mayor Woody Goodman, Keith examines a video that was taken, apparently by a stalker, inside of Woody's house. Also, Wallace goes to the school's Sadie Hawkins dance with Jane, and Mac asks Veronica for advice on how to improve her less-than-romantic relationship with Beaver.
A restless Veronica is plagued by dreams in which the students killed in the bus crash confront her. Meanwhile, Logan and Wallace are paired together for a physics project that neither is enthusiastic about, until they discover that their success might help Veronica receive a scholarship. Later, when a large number of students are diagnosed with a medical ailment that gives them the right to postpone school tests and projects, a concerned principal Clemmons hires Keith to investigate the validity of the disorder.
Veronica looks for a dog killer after being hired by a student whose pet was ran over, and Keith discovers surprising revelations about Kendall's past. Meanwhile, Weevil learns that the Fitzpatricks are abusing his old gang members, and Jackie applies for a job at Java the Hut and asks Veronica to put in a good word for her. Wallace tries to get back together with Jackie, but she gives him some heartbreaking news.
Gia is convinced she's being stalked, so Veronica takes the case despite her dad's orders not to get involved, but what she discovers not only shocks both girls, but leads to further questions. Meanwhile, Woody enlists Keith's help in avoiding a scandal when he ends up with a passed-out woman in his motel room. Also, when Principal Clemmons cancels the prom because of drinking violations on the senior trip, Logan takes it upon himself to throw an "alterna-prom" in his Neptune Grand suite.
As Aaron Echolls's trial is about to conclude, tensions rise as Veronica, Keith and Logan take the witness stand to testify against him. Meanwhile, after Veronica finds a suspicious e-mail in Woody's computer, Keith turns to Lamb with evidence to arrest Woody, but Lamb refuses, believing that Keith is trying to turn him into a laughing stock. Also, to everyone's surprise, Lucky brings a gun into school with the intent to find Gia.
The second season ends as Veronica, on her graduation day, learns who is responsible for the bus crash. After uncovering the culprit, her life is endangered as she tries to warn those closest to the killer. Also, Wallace learns some surprising information about Jackie, Keith enlists Veronica's help in his ongoing investigation of Woody, and the seniors celebrate their graduation with a lavish party at the Neptune Grand.
Veronica is in true form from the moment she and boyfriend Logan, along with close friends Wallace and Mac, set foot on the campus of Hearst College. Wallace enlists Veronica's help when his new roommate, Piz, has all his belongings stolen. While working on Piz's case, Veronica learns that the campus serial rapist has struck again. Meanwhile, Keith runs into trouble while transporting a recently released convict across the country to reunite him with Kendall.
Veronica is hired by the campus newspaper to do an undercover expose on the Zeta Theta sorority sisters during rush week to investigate Parker's rape. Throughout the investigation, Veronica realizes that everything is not exactly what as seems in the sorority house. Meanwhile, Logan and Wallace participate in a prisoner/guard role-playing experiment for their Sociology class, which challenges them psychologically.
Veronica is hired by by a Hearst football player to help him find his stolen playbook before the next practice, or risk losing his scholarship. As a result of the expose Veronica wrote about the campus sorority, Dean O'Dell threatens to expel her if she doesn't reveal one of her sources. Logan tells Veronica his schedule is keeping them apart, but she realizes he has been spending time participating in illegal gambling. Meanwhile, Veronica convinces Keith to hire Weevil to assist with office work at Mars Investigations.
When Logan is informed that his inheritance is running low, he become suspicious and enlists Veronica's help to sort through his financial records. Veronica uncovers that large sums of money have been going to a man named Charlie Stone. Meanwhile, Keith is hired by Harmony to investigate her cheating husband.
It's Halloween at Hearst and while Veronica is looking for Logan at the underground campus casino, the place is robbed and the thieves take Veronica's necklace, given to her by Lilly Kane. Meanwhile, Dean O'Dell and his wife Mindy seek Keith's help in tracking down Steve, the biological father of Mindy's son, who is deathly ill. Wallace, distracted by a new group of friends, struggles to pass his Mechanical Engineering class.
Veronica is accused of plagiarizing her paper for Professor Landry's criminology class. In trying to clear herself, she discovers that her mentor is not who she thought he was. Wallace is pardoned by Dean O'Dell for cheating on his exam, but makes a decision that could affect his college career. Piz invites Veronica to a night of bowling and she decides to bring Logan and Parker, unaware Piz wanted the evening to be more of a date.
Veronica is disappointed in Keith for his ongoing relationship with his client, Harmony, who invites him on a romantic weekend getaway. When Veronica retreats to Wallace and Piz's dorm room for some quiet time, Logan seeks her help in clearing Mercer of the rape charges, but refuses to give her his alibi.
Selma Rose, the wealthy grand-daughter of the founder of Hearst College and a member of the Hearst College Board of Trustees, mysteriously disappears the night before she is to cast a swing vote that will determine the fate of the Greek system on campus. Keith, with Veronica's help, is hired by Dean O'Dell to investigate the disappearance. Meanwhile, Veronica has been rehired as a photographer at the Hearst Free Press, but she and Logan fight over her involvement in the rape case.
Dean O'Dell reinstates the Greek system on campus and, determined to solve the campus rape case, Veronica, along with Mac, Wallace and Piz, attends a party armed with coasters designed to test for drugs in the drinks of her peers. Meanwhile, Dean O'Dell hires Keith to investigate whether or not his wife is cheating on him.