After the summer fireworks caused by a dangerous confrontation with Lilly Kane's murderer and a surprising visitor at her door, Veronica attempts to settle into "normal" life, complete with a new after-school job and a return to the popular fold at Neptune High, but she gets pulled back into the investigation business when Wallace is kicked off the basketball team for testing positive for drugs.Meanwhile, Keith sits down with reporter Julie Chen to discuss his new book on the Lilly Kane murder, "Big Murder, Small Town." Later, after seeing his father arrested for murder and being charged and tried for murder himself, Logan seeks refuge from the paparazzi and relaxes poolside at the Casablancas mansion with buddies Dick and "Beaver" and their sexy stepmother Kendall.

After tragedy strikes Neptune, Calif. and the local sheriff rushes to judgment, an emotional Veronica attempts to help a grieving family member rule out suicide as a contributing cause in the calamity. Meanwhile, Wallace offers to help transfer student Jackie Cook, the fiery, flirty daughter of professional baseball player Terrence Cook, track down the person who damaged her car in the school lot. Later, mayoral candidate Woody Goodman asks Keith to consider running for sheriff.

Deciding to give Jackie the benefit of the doubt since she's dating Wallace, Veronica tries to help Jackie determine who stole her credit card, leading Veronica to appear on a psychic's community access show to pursue a lead. Meanwhile, Wallace confronts his mother Alicia about who his real father is. Later, Veronica learns of a voice mail recording from one of the students that died, made at the moment the bus crash.

When the profits from the Neptune High Winter Carnival go missing, Veronica finds herself defending Jackie from the condemning teachers and students. Meanwhile, Keith meets with her father, Terrence Cook, after he is accused of playing a role in the bus crash, and Logan initiates a new relationship while Beaver continues an old one.

When a private website for Neptune High's gay students is hacked, and the members blackmailed, Veronica finds it difficult to track down the culprit when the victims want to remain anonymous. Meanwhile, Hannah finds out Logan's true intentions, and Keith believes he has found an alibi for Terrence.

Gia enlists Veronica's help to find out who is stalking her, and Clemmons cancels the senior prom.

Veronica takes the stand in Aaron Echolls's murder trial, and is distracted during final exams while waiting for the verdict. Meanwhile, Keith takes new evidence about the mayor to Lamb, and Weevil asks Mac and Cassidy for help to pass algebra.