While trying to navigate the everyday drama of high school, the smart, fearless, 17-year-old Veronica Mars also moonlights as an apprentice private investigator out to solve her wealthy town of Neptune's toughest mysteries. After coming to the aid of the new kid, sophomore Wallace Fennel, who's been duct-taped to the school's flagpole, Veronica ends up incurring the wrath of the thugs who put him there, Eli "Weevil" Navarro and his P.C.H. Biker Boyz. To get Weevil and his gang off her and Wallace's case, Veronica devises an intricate plan that helps some of Weevil's cronies avoid trouble with the law.

Meanwhile, defying her father, Keith Mars, the disgraced former sheriff turned private eye, Veronica pursues a late-night case of adultery against billionaire Jake Kane, only to make an unsettling discovery about her mother, who abandoned Veronica and Keith a year ago.

Veronica investigates possible fraud in the election of student council president at school after Duncan wins, beating a more popular, but less affluent student who promised to eliminate the wealthy students' on-campus perks.

Meanwhile, Logan causes a public relations nightmare for his movie star parents Aaron and Lynn Echolls when footage of him organizing boxing matches between homeless men is posted on the internet and leaked to the media. Later, Veronica and Keith learn that the man who admitted to murdering Lilly is set to be executed, but a second look at crime scene photographs puts his confession in question.

A series of fire drills leads Veronica to discover that Neptune High has been receiving bomb threats, so she enlists Wallace and Mac's help to investigate classmates who could pose a serious threat to the school, including new student Ben.

Meanwhile, Keith stuns Veronica with the news of who he's been secretly dating. Later, Duncan confronts Veronica about her ongoing investigation into his sister's death.

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.

After discovering the true perpetrator of the bus crash, Veronica is desperate to warn others before it's too late. However, she inadvertently puts herself and her loved ones at risk in the process.

Meanwhile, Keith tracks down Woody in hiding, Wallace leaves for Paris to be with Jackie, and Weevil again runs into trouble with the law.