To help restore a cheerleader's ruined reputation, Veronica turns to funky computer geek Mac to find the hacker responsible for leaking the embarrassing, private results of a popular online "purity test" to all of Neptune High. Meanwhile, Keith helps Wallace and his mom with an unruly tenant in their building. Later, to get answers about Lilly's murder, Veronica attempts to visit Lilly's confessed, condemned killer Abel Koontz in prison.

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.

When a classmate's boyfriend threatens to post a humiliating video of the girl online if she dumps him, Veronica helps her concoct a scheme to ensure "mutually assured destruction" if he doesn't allow the relationship to end peacefully.

Meanwhile, Keith begins to search for Duncan after his parents post a huge reward for information on his whereabouts. Later, as her secret new relationship heats up, Veronica learns a disturbing new fact about the night that she was drugged and assaulted.

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.

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.

While dealing with her own feelings of jealousy regarding Duncan, Veronica helps a young woman who believes that her new fiancée is secretly after her fortune by sifting through his background and even posing as a sexy, available coed to entrap the guy.

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.

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.