Set in the fictional town of Neptune, the pilot introduces Veronica, a high-school student moonlighting as a private investigator under the wing of her detective father. Two separate mysteries are presented in the episode, which are explored throughout the season and resolved in the final and penultimate episodes
Veronica Mars begins her junior year at Neptune High trying to re-adjust her life after her boyfriend, Duncan Kane, left her and after the murder of her best friend, Lilly Kane the previous year. While helping her father, private investigator Keith Mars of Mars Investigations, investigate the possibility Jake Kane, father of Duncan Kane and Lily Kane, is having an affair with another woman, Veronica discovers more clues related to the Lilly Kane Murder Case. Veronica decides to find Lilly Kane's true killer and discover who raped her a year earlier.
Flashbacks reveal Veronica's backstory: in small-town Neptune, California, Veronica - daughter of well-respected County Sheriff Keith Mars is a typical teen who was dating Duncan Kane, and was popular with loving parents. But when her best friend and Duncan's sister, Lilly Kane, is murdered, Veronica's life falls apart. Keith accuses software billionaire Jake Kane, Lilly's father, of being involved in the murder. This provokes Neptune's wrath, and Keith is ousted from office and replaced by Don Lamb in a recall election. Veronica's mother, Lianne Mars, unable to face the loss of status and economic security, develops a drinking problem and suddenly leaves town. Veronica's boyfriend also ends their relationship, and her friends turn their backs on her. To prove that she is unaffected by the rejection, Veronica attends wealthy classmate Shelly Pomroy's "09er" party. Her drink is spiked with GHB and she is raped, but Sheriff Lamb refuses to take her report seriously. These events shock Veronica and she changes her attitude towards her former friends, becoming tough and cynical.
Estranged from all her "09er" friends—wealthy students from the fictional 90909 ZIP code—including Duncan and Lilly's ex-boyfriend, Logan Echolls, and feeling the drop in income and status that her father's dismissal from office brings, Veronica takes a part-time job in her father's newly opened private investigation agency, Mars Investigations. Although the case of Lilly's murder is officially closed following the confession of a former Kane Software employee, Abel Koontz, Veronica continues her own investigation into what happened. Her investigation discovers new evidence which suggests that Koontz is innocent.
In the present, Veronica starts her Junior year at Neptune High by freeing new student Wallace Fennel, who had been stripped and duct-taped to the school flag pole. Wallace explains that while working at the local Sac-n-Pac, he alerted the sheriff's department to two PCH (Pacific Coast Highway) bikers who took alcohol without paying. Sheriff Lamb exposes Wallace as the witness, and despite Wallace's attempts to retract his accusation, Lamb walks away with proof from the in-store video camera. Wallace's duct-taping is PCH retribution for his honesty. In a convoluted scheme to help Wallace, Veronica sets up Logan by placing a bong in his locker. Once the bong is taken to the evidence room at the sheriff's department, Veronica triggers it to smoke and spark by remote control, leading to the arrival of the fire department. The fire chief, a friend of Veronica, switches the video from the Sac-n-Pac with one Veronica filmed of a deputy receiving sexual favors. When the bikers are in court, that video is shown instead, embarrassing Lamb and undermining the case against the bikers. Wallace is forgiven and Eli Weevil Navarro, the bikers' leader, becomes Veronica's occasional ally.
At Mars Investigations, Duncan and Lilly's mother, Celeste Kane hires Keith to ascertain if her husband Jake is having an affair, despite her open contempt for both Keith and Veronica. Keith is busy with other projects, and Veronica takes it upon herself to follow Jake. Veronica takes photos of him at the Camelot Motel as he meets with an unseen woman after midnight. Once Keith sees the license plate number of the woman's car, he stops the investigation and files the photograph. Puzzled by his actions, Veronica finds the file and learns that Keith has continued his own personal investigation of Lilly's murder. Veronica discovers that the car belongs to her missing mother, Lianne, and begins to investigate the murder herself.
- The two main mysteries of the season--Lilly Kane's Murder and Veronica's Rape--are set up.
- All of the main characters are introduced, including Duncan Kane, Logan Echolls, Eli “Weevil” Navarro, Wallace Fennel, Keith Mars, Lilly Kane (deceased), and Veronica herself.
- Veronica finds out that it was her mother who was at the Camelot motel with Jake Kane, and that her father was still investigating Lilly Kane's murder.
- Kristen Bell as Veronica Mars
- Percy Daggs III as Wallace Fennel
- Teddy Dunn as Duncan Kane
- Jason Dohring as Logan Echolls
- Francis Capra as Eli "Weevil" Navarro
- Enrico Colantoni as Keith Mars
- Michael Muhney as Don Lamb
- Corinne Bohrer as Lianne Mars
- Amanda Seyfried as Lilly Kane
- Lisa Thornhill as Celeste Kane
- Kyle Secor as Jake Kane
- "La Femme d'Argent" — Air [DVD only - not in original broadcast]
- "What You Want" — The Wayouts
- "Insincere Because I" — The Dandy Warhols
- "Sitt'n on Top of the World" — Botany Boyz
- "Just Another" — Pete Yorn
- "White Lines (Don't Don't Do It)" — Grandmaster Flash
- "Give You More" — Taxi Doll
- "Girls" — Death in Vegas
- "Bathroom Stall" — DAMe Lee
- "Weak Become Heroes" — The Streets
- "(Don't Fear) The Reaper" — Blue Öyster Cult
- "Pata Pata" — Miriam Makeba
- "Atomic Girl" — Wannabes
- "Butterflies" — Davíd Garza
- "All You Need Is Love" — The Beatles [Played on music box.]
- In the produced version of the "Pilot" episode, Lilly Kane is found by the pool in the same spot where she was murdered. However, series creator Rob Thomas indicated that this was not originally where Lilly's body was to be found, and the location was changed for plot consistency. 
- The original cut of the episode is somewhat longer than the broadcast version. The original version appears in its entirety, featuring all of Piznarski and Thomas' original sequences on the DVD release of Season One.
- In the original pilot, Lilly's body was dumped into a river and found later. But after the pilot was picked up by a cable network instead of HBO, Showtime or FX the network found this a little too disturbing, especially because it involved Jake Kane disposing of his own daughter's body and decided to have her body be found on the Kane property.
- Rob Thomas was so impressed with Jason Dohring's acting that a scene of a tearful Logan confronting Veronica after Lilly's death was added to the script after the actor was cast.
- The pilot script describes Veronica the following way: "She is not cute. She is sexy. Tough. Prematurely jaded. Angelina Jolie at 17."
- The scene in which Veronica wakes up after being raped was longer and more graphic and was edited down by the censors.
- Amanda Noret, who plays Madison Sinclair, and the girl who plays Shelly Pomroy (who is not a working actress but has appeared in over eleven episodes), are cousins in real life.
- It is critical to the entire storyline that Lilly's shoes were in a photo taken the night of the murder. We see the new sheriff holding up the evidence bag on TV in the first episode of season one and the shoes in the bag are flip flops. The rest of the season they are graffiti-ed tennis shoes.
- The dog, Backup, is white with brown spots in the first season. During season 3, Backup is almost entirely reddish brown.
- After Weevil smashes the 09ers' car with the crowbar, Logan and friends drive off. While Weevil is then talking to Veronica, the car is still parked behind them, but in the next shot it's gone again.
- After Logan bashes Veronica's car and Weevil asks him to apologize, Logan's arm goes from his hip to his head in between shots.
- During Veronica's flashback of the morning after her rape, she fixes the left strap on her dress. In the next scene her strap is broken again.