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 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.

With only a commonplace name, an old address and dim memories as leads, Veronica and Wallace attempt to help classmate Justin Smith find his father John, who disappeared 10 years earlier.

Meanwhile, as Veronica faces some complicated feelings towards ex-boyfriend Duncan and new romantic interest Troy, guidance counselor Rebecca James calls Keith to the school to discuss the recent, dramatic changes in his daughter's life. Later, Duncan struggles with ways to cope with his sister's death as the anniversary of her murder approaches.

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 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.

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.

After being hired by hip-hop heavyweight Percy "Bone" Hamilton to find his kidnapped daughter, Veronica and Keith look to the music mogul's long list of enemies, family members and the girl's Neptune High social circle for clues on her whereabouts. Meanwhile, following Lynn Echolls' apparent suicide, Logan cynically endures his father Aaron's effusive displays of grief as they prepare for her memorial ceremony.

Veronica investigates who at school is doing everything possible to distract Sabrina from studying and wreck her grades in an obvious attempt to sabotage her chances at becoming valedictorian.

Meanwhile, an unsavory, rival private investigator makes Keith a business offer. Later, Veronica pursues a risky lead that could discredit Abel Koontz's confession, as Logan stumbles onto her detailed files on everyone connected to Lilly's murder.

While helping her classmate Mandy search for her missing Jack Russell terrier, Veronica stumbles onto a bigger mystery, which affects pets all over Neptune.

Meanwhile, tensions mount in the Echolls family as Trina tries to convince the now-retired Aaron to take a part in her new boyfriend's independent movie. Later, Weevil is arrested for breaking into the Kane residence and taking something from Lilly's room.

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.