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 tries to help her new boyfriend Troy find his father's stolen car and turns to Weevil for assistance, but the situation becomes dangerous when she discovers that Logan and Troy's buddy Luke might have left more than a piata in the car after their night out in Tijuana.

While Keith has accepted that his wife is gone and begins dating school guidance counselor Rebecca James, Veronica continues to secretly investigate her mother's whereabouts, leading her to stumble on a secret Lianne Mars was keeping.

Veronica surprisingly finds herself working as a "love detective" when she's asked to track down her friend Meg's secret admirer and a Russian bride's estranged fiancé.

Meanwhile, after discovering that one of Lynn Echolls' credit cards is in use, Veronica and Logan go to a Los Angeles hotel in hopes of finding her or a clue.

Following an emotional reunion with her mother, Veronica is hired to track down Neptune High's beloved mascot, Polly the Parrot, which was apparently kidnapped by a rival school on the eve of a big basketball game.

Meanwhile, with her suspicions about the Kane family rekindled, Veronica attempts to gain access to her father's original interrogation tapes. Later, Veronica's relationship with Deputy Leo heats up, as does Meg's relationship with Duncan.

Determined to get to the truth behind who drugged and assaulted her at a party the year before, Veronica questions her friends and many rivals about the chain of events that night at Shelley Pomroy's house. Meanwhile, when one of Veronica and Wallace's stunts affects her job at Kane Software, Alicia confronts Keith about his daughter's behavior. Later, in an attempt to get closer to his son, Aaron throws a birthday party for Logan that inadvertently surprises everyone.

In the shocking, action-packed season finale, a determined Veronica must betray someone she cares deeply about in order to solve the season-long mystery of who murdered her best friend Lilly Kane, but what she discovers puts her life in serious danger. Meanwhile, on the eve of a reception for the Governor of Calif., Jake Kane asks Duncan if he really wants to know what happened on the night Lilly died. Later, Keith awaits the results of a paternity test.

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.