In an effort to help Wallace's new crush Georgia, who was duped out of her money in an internet scheme, Veronica must outwit a group of computer "thugs," known as the Silicon Mafia.

Meanwhile, Keith makes Veronica introduce him to her new boyfriend Troy before allowing her to go to the homecoming dance with him. Later, Logan helps Duncan edit together a memorial video for a school dedication ceremony marking the one-year anniversary of Lilly's death. The dance and the video bring back Veronica's memories of when the four of them were friends.

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.

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.

While accompanying Wallace to Hearst College, she runs into her ex, Troy Vandergraff, who enlists her help when he is accused of date rape. Meanwhile, Keith helps Cliff with a personal problem involving a prostitute, and Logan makes a decision regarding his relationship with Hannah.

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

When Veronica's term paper appears on the internet, she is accused of cheating by the TA and must prove her innocence. Meanwhile, Wallace has problems of his own when long basketball practices distract him from his studies, and Keith begins seeing Harmony Chase.

When Veronica discovers Timothy Foyle breaking into Mars Investigations, she uses his help to track down Dean O'Dell's true killer. Meanwhile, Logan and Parker's relationship takes an unexpected turn, and acting Sheriff Mars brings another murderer to justice.

As the end of the first semester at Hearst College draws to an end, the election for sheriff in Neptune comes to a close and Veronica and Piz discuss the effect a summer apart will have on their relationship.

Veronica and Keith launch their investigation. Their involvement puts Police Chief Langdon on edge. Penn goes public with his theory on who the bomber is. Meanwhile, local teen Matty Ross begins her own search for her father’s killer.