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.

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 the campus rapist anonymously announces the location of his next rape, Veronica hires her friends to help her track him down, but is shocked when she discovers the rapist's identity. Meanwhile, Logan makes a drastic decision about his future with Veronica, and Dean O'Dell hires Keith to prove that his wife is unfaithful.

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.

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.

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.

Veronica debates coming clean to Nicole. Veronica’s fidelity is tested. Veronica and Keith discover they aren’t the only ones who believe they’ve found the bomber. A surprising potential client tries to hire Mars Investigations.

When Duncan disappears with Meg's baby, Lamb must work with two FBI agents to extract as much information as possible from an uncooperative Veronica. Meanwhile, Wallace reveals the real reason he returned to Neptune, and Weevil and Logan make a breakthrough in their hunt for the rogue gang member.

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.

Weevil asks Veronica to clear his name after he's arrested for selling fake debit cards to Hearst students, claiming he's being framed because of his criminal background.

Convinced the bomber is still at large, Veronica visits Chino to learn more about Clyde and Big Dick. Mayor Dobbins’ request for help from the FBI brings an old flame to Neptune. Veronica confronts her mugger.

As Veronica learns more about Nicole's past, her suspicion deepens. A frantic phone call from Paris leads to a search for Matty. Veronica unwittingly does legwork for Leo.

Veronica uncovers information that her fellow outcast Mac was switched at birth with a more affluent student, causing Veronica to examine her own questions about whom her real father may be. Meanwhile, a serial killer has resurfaced in Neptune forcing Sheriff Lamb to forge a reluctant, tense partnership with Keith. Later, Veronica flirts with a handsome young rookie at the sheriff's department to obtain more information on Lilly's murder.

Veronica takes the stand in Aaron Echolls's murder trial, and is distracted during final exams while waiting for the verdict. Meanwhile, Keith takes new evidence about the mayor to Lamb, and Weevil asks Mac and Cassidy for help to pass algebra.

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.

Panic spreads through Neptune when a bomb goes off during spring break. Veronica and Keith are hired by the wealthy family of one victim injured in the bombing to find out who is responsible.

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.

Veronica and Keith’s client, Daniel Maloof, makes a shocking confession. Sheriff Langdon closes in on her top suspect. Veronica and Matty join forces, just as the whole investigation is flipped on its head.

Veronica discovers Keith has been hiding something scary from her. The real reason for Penn’s latest theory on the bomber comes to light. Veronica loses confidence in new friend, Nicole, owner of Comrade Quacks.

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.

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.

When Veronica is released from jail, she is contacted by Josh Barry who is desperate to prove his innocence in his father's murder. Meanwhile, Keith gets bittersweet news from the county commissioner, and Logan helps Mac and Parker on a scavenger hunt.

Veronica doesn't believe the evidence adds up against Weevil, who has confessed to stealing credit card applications from Logan's family, and launches an investigation to help her new ally. Meanwhile, after joining Ms. Mallory Dent's newspaper class, Veronica clashes with socialite Caitlin Ford, Logan's bombshell girlfriend, but is intrigued by the attention shown to her by another wealthy student, Troy Vandegraff, a friend of ex-boyfriend Duncan. Later, Veronica learns that Lilly got a ticket driving her car on the day she died -- two hours after her supposed time of death.

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.

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.