Veronica spends the summer trying to become “normal” again, but finds it difficult when Wallace is kicked off the basketball team for testing positive for drugs. Meanwhile, Keith is finding it hard to cope with popularity after releasing his book on the Lilly Kane murder, Logan takes refuge from the paparazzi at Dick and Beaver's, and a field trip to the local sports arena has shocking consequences.
Veronica finds her life once again swirling out of control as she struggles to deal with the aftermath of the bus crash by helping the daughter of the bus driver rule out suicide. Meanwhile, new student Jackie gets the attention of Wallace, who does a little detective work of his own.
Beaver hires Veronica to investigate his stepmother, Kendall, who he believes is cheating on his dad and planning to clean him out, but both are shocked by what they discover. Meanwhile, Wallace begins dating Jackie, against Veronica's advice.
Veronica tries to get her mind off the bus crash by going undercover to help a wealthy woman who is determined to prove that her husband is cheating on her. Meanwhile, Keith asks Alicia about the mysterious man who recognized her in Chicago, and Weevil gives Veronica new information about the accident.
Despite the fact that she dislikes Jackie, Veronica helps her find out who stole her credit card by going on a local psychic TV show. Meanwhile, Wallace's world is turned upside-down when his real father returns home, and Veronica gets a huge piece of new evidence in the bus case.
Veronica is shocked when a dying Abel Koontz shows up asking for her help in finding his missing daughter before he dies. Meanwhile, Logan is reunited with his father when he his arrested for Felix's murder, and Keith waits for the results of the election.
Veronica goes undercover after Duncan comes to her with a plea to help him find out which one of the children Meg was babysitting was being mentally abused by their parents. Meanwhile, Dick, Beaver and Kendall are visited by their lawyer, who informs them of Big Dick's wishes.
Veronica helps Keith determine who is haunting a school bus crash victim's parents, who are currently embroiled in a suit against the school district. Meanwhile, after Logan asks for help fighting the murder charge against him, Veronica stumbles into a dangerous situation with the local Irish mob. Later, Weevil's leadership of the P.C.H. Bikers is put into question.
After finding her mother's old permanent record at school, Veronica wonders how well she knew her mother at all, and decides to investigate her mother's school friends. Meanwhile, Trina takes the role of director in the school play, and while she has a confrontation with Kendall, Veronica has one with Celeste.
Veronica's day goes from bad to worse as she is called for jury duty over a case involving two 09ers and a Hispanic woman, but finds that Neptune is even more divided than she thought. Meanwhile, Keith helps Lamb track down the missing sex tapes, the key piece of evidence in the Aaron Echolls trial.
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.
Veronica loses all $12,000 for her class's senior trip when a cash box in her possession is stolen 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.