The finale concludes the storyline of Lilly Kane's murder, as Veronica Mars finally discovers the identity of the murderer after investigating the mystery with her father Keith Mars throughout the season.
The first season revolves around Veronica's investigation of her best friend Lilly's murder. Prior to the murder, Veronica was dumped by her boyfriend, Duncan Kane who was also Lilly's brother. After Lilly was killed, Veronica's father, County Sheriff Keith Mars, accused Lilly's father, popular software billionaire Jake Kane, of being involved in the murder. This provoked Neptune's wrath and Keith's ousting as sheriff in a recall election. Veronica's mother, Lianne Mars, developed a drinking problem and left town. Veronica's "09er" friends—wealthy students from the fictional 90909 ZIP code—forced her to choose between them and her father; Veronica chose her father.
After being voted out as sheriff, Keith opens a private investigation agency, Mars Investigations, where Veronica works part-time. Veronica helps her father solve cases and conducts her own investigations on behalf of friends and acquaintances at school. Veronica discovers new evidence which suggests that Abel Koontz, the man imprisoned after confessing to Lilly's murder, is innocent. As Veronica delves deeper into the murder case, she also works on other investigations, seeks her mother's whereabouts and deals with the aftermath of being drugged and raped during an "09er" party. Things get more complicated when Veronica falls into a relationship with Lilly's ex-boyfriend Logan Echolls, who for a time held Veronica partly responsible for Lilly's death and went out of his way to harass her.
In the previous episode, Keith proves the innocence of convicted murderer Koontz, who had falsely confessed to murdering Lilly. Veronica, who believed that she had been raped the previous year at a party, discovers that she and Duncan had sex while under the influence of GHB; Duncan left that next morning because he believed Veronica was his sister. Veronica spends time with her boyfriend Logan in his pool house, but discovers a hidden video system linking to cameras focused on the bed. Veronica is shocked and goes home, only to find her mother Lianne has returned from rehab.
When a reporter writes an article about Koontz's innocence, Duncan demands the truth from his parents, Jake Kane and Celeste Kane, who tell him that they arrived home one night to find Duncan covered in blood and holding Lilly's body. Cassidy Casablancas tells Veronica that on the weekend of Lilly's murder, he had gone surfing in Mexico with Logan and Dick Casablancas; however, Logan had driven back to Neptune to see Lilly. Veronica and Keith discover that a shot glass Logan bought is on the evidence record of Lilly's bedroom and car. Talking to Keith on the phone, Veronica suggests that Logan is the murderer, and their conversation is overheard by the leader of the Latino biker gang PCHers, Eli Weevil Navarro, who had a relationship with Lilly.
Keith ends his relationship with Wallace's mother Alicia Fennel to give Lianne Mars a second chance. Because Celeste refused to pay the $50,000 reward for finding Duncan, Keith sues the Kanes, who agree to pay if Veronica signs away any future claim to their estate. Once Veronica signs, Keith shows her the DNA test that proves he is her father, meaning Veronica never had a claim of the estate. Logan is arrested, and once released he angrily breaks up with Veronica for providing the evidence against him. Logan then explains that when he saw Lilly after returning from Mexico, he knew their relationship was over and wrote a letter which he left in her car.
Veronica realizes that Logan's letter was never found, and searches Lilly's room during a dinner party at the Kane's household. Duncan enters the room and they discover several videotapes which show Lilly having an affair with Logan's father, Aaron Echolls. Veronica believes that Lilly found the tapes and refused to return them, which angered Aaron and he killed her; Duncan arrived home to find Lilly dead and had an epileptic fit, at which time Jake and Celeste returned home. While an unseen person watches them from a closet, Veronica calls Keith and tells him that she will bring home the tapes, noting that Aaron is at the party. Before she leaves, Veronica tells Duncan that they are not related. Meanwhile, Logan is drunk and stands on a bridge railing. Weevil and the PCHers arrive and they initiate a fight.
While driving home, Veronica discovers Aaron in the back seat of her car and crashes into a power pole. Although both are knocked unconscious, Veronica awakens first and distributes the tapes around a nearby house. Aaron traps Veronica in a fridge, and when Keith arrives, he lights it on fire. Keith is burnt freeing Veronica, and Aaron is hit by a truck while trying to escape. The police arrive and Keith and Aaron are taken away on stretchers as Aaron is read his rights. Jake vows to see Aaron fry for his actions and is also arrested for obstruction of justice. Keith wakes up in hospital to find Alicia by his side. Veronica arrives home and tells her mother to leave before Keith comes home; she knows that Lianne is still drinking and did not finish her rehab. Lianne packs her bags and steals the $50,000 settlement check from the Kanes before she leaves. Veronica dreams about her and Lilly floating on a pool raft in a pool full of flowers, and they say their final goodbyes. Veronica wakes up and answers the door, and tells the unseen person, "I was hoping it would be you".
- Keith gets back the test results and tells Veronica that he is definitely her father.
- Logan wasn't in Mexico the day of Lilly's murder. He came back to Neptune to talk to her, but just left a note and a shot glass in her car.
- Lilly and Aaron Echolls were having an affair. She found tapes of them having sex and stole them. He chased after her and when she refused to give him the tapes, he hit her with an ashtray, killing her.
- Aaron tries to escape but is hit by a flower truck with a picture of a lily on the side.
- Veronica confronts her mother. She knows her mother left rehab, so she asks her to leave. Lianne steals Keith's $50,000 check.
- 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
- Amanda Seyfried as Lilly Kane
- Erica Gimpel as Alicia Fennel
- Corinne Bohrer as Lianne Mars
- Lisa Thornhill as Celeste Kane
- Daran Norris as Cliff McCormack
- Michael Muhney as Don Lamb
- Kyle Gallner as Cassidy Casablancas
- Jennifer Gareis as Deborah Collins
- Steve Rankin as Lloyd Blankenship
- Harry Hamlin as Aaron Echolls
- Kyle Secor as Jake Kane
- "Where the Boys Are" - Connie Francis
- "La Bamba" - Mariachi Vargas De Tecalitlán
- "Bad Boyfriend" - Garbage
- "Wannabe" - Spice Girls
- "Lily Dreams On" - Cotton Mather
- Wallace: My "blonde pulling me into the girls bathroom" fantasy? Ruined.
- Veronica, Wallace: [simultaneously] Do me a favor?
- Aaron: Whoa, whoa, whoa. You can't just barge in here!
- Lamb: Now, come on now. What? You've been in like, what, thirty cop movies?
- Veronica: Isn't it better, like this?
- Lilly: So much better.
- Veronica: This is how it's supposed to be.
- Lilly: Totally.
- Veronica: This is how it's gonna be. From now on. Right? Lilly?
- This was the lowest rated prime-time series to ever get renewed for a second season. It was also the only new drama to survive UPN's 2004-2005 TV season.
- Logan's final shot is of him giving the PCHers a kung-fu "bring it on" gesture. According to Rob Thomas, this was improvised by Jason Dohring during filming.
- We see a truck with the name Thomas written on the side, as a nod to creator and executive producer Rob Thomas. Also of note, the flower on the truck is a Lily.
- There is a mugshot of actor/stuntman Thomas Rosales, Jr. on the wall of the sheriff's station, it can be seen when Logan calls Veronica on his cell phone.
- The episode's title is a reference to the late 1950s/early 1960s sitcom Leave It to Beaver.
- When Keith rams into Aaron Echolls with the crutch, Keith's right hand is down near the crutch's base. In the next shot his hand has moved up near the crosspiece handle.
- When Keith runs into the fire to rescue Veronica, a man and a woman can be seen calmly standing behind him, presumably members of the production crew.