Meet Veronica Mars. Your typical high school student and private eye. A year ago, Veronica's best friend Lilly was murdered. Her father, Keith, then the town sheriff, accused Lilly's billionaire father of the murder. When another man confessed, Keith was booted from office. All of Veronica's friends stopped talking to her, and her mother left town. But as Veronica starts her junior year of high school, it becomes clear that nothing about her life is what it seems.
When Weevil's grandmother is arrested for credit card fraud, Veronica and Wallace reluctantly help the investigation to clear her name. Meanwhile, Logan's new girlfriend, Caitlin Ford, joins the 09ers in making Veronica's life difficult, while a new arrival in town, Troy Vandegraff, tries to get to know her better.
Veronica tries to help a classmate track down his long lost father, but with very little to go on, she finds the task more daunting than she thought. Meanwhile, Keith meets with school guidance counselor Rebecca James to discuss Veronica's feelings about Lilly's murder.
In an attempt to help out Wallace win over a potential girlfriend, Veronica takes on the case of tracking down an Internet fraud ring, which leads her to an underground gaming community. Meanwhile, Logan agrees to assemble a video of Lilly to mark the one-year anniversary of her death, and Troy becomes closer to Veronica.
After a night in Tijuana, Troy finds himself in a tough situation when his car is stolen and turns to Veronica for help. But what she finds changes her relationship with him. Meanwhile, Keith and Rebecca begin dating against Veronica's wishes, and Veronica makes another shocking discovery about her mother.
The tension between the 09ers and non-09ers comes to a head when the school elections appear to be rigged. Veronica helps Wanda, the underdog, campaign to beat Duncan, despite her feelings for him. Meanwhile, Logan clashes with his father, movie star Aaron Echolls, when he is caught in the press engaging in unruly behavior.
Veronica becomes suspicious when a young pregnant woman who lives in their apartment complex 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 that her mother and Jake Kane were high-school sweethearts.
A purity test being passed around Neptune High leaves Veronica's friend Meg humiliated, which leads Veronica to uncover who would want to ruin the reputation of the nicest girl in school. Meanwhile, Keith helps Wallace's mom with a tenant who refuses to leave, and Veronica has a shocking meeting with Lilly's confessed killer.
Against her father's wishes, Veronica infiltrates what she believes to be a cult in order to investigate a classmate's sudden change in personality. But after meeting the people in the cult, she begins feel like she is making a mistake. Meanwhile, her investigations into Abel Koontz's claims about her family continue.
A holiday poker game at Logan's house gets nasty when Weevil's winnings disappear, leaving Veronica to determine the guilty party before Weevil finds his own way of getting the money back. Meanwhile, Keith helps Lynn Echolls find out who is sending threatening messages to her husband, Aaron, before their big Christmas party.