Veronica becomes suspicious when a young pregnant woman who lives in their apartment complex with her volatile boyfriend suddenly disappears; fearing the worst, Keith steps in to help his daughter investigate this case for the girl's estranged parents.

Meanwhile, Logan and Weevil get thrown into detention together after arguing with a teacher, leading the rivals to discover some surprising things in common. Later, while working on an alumni photo project in her journalism class, Veronica is shocked to discover in the '79 yearbook that her mother and Jake Kane were high-school sweethearts.

When one of Neptune High's haughtier students brings a sexual harassment suit against a favorite teacher, Veronica finds herself pitted against her father when the girl's parents hire Keith to help in their case. Meanwhile, with the tabloids claiming his mom is still alive, Logan turns to Veronica to help him track down the truth. Later, Veronica discovers more unsettling information about Duncan's hidden medical condition.

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.