Veronica gets settled into college life and helps Wallace's roommate, Piz, discover who stole a prized guitar and other possessions out of his car. Also, a serial rapist strikes again, and Keith picks up a just released Cormac Fitzpatrick from prison and takes him to meet Kendall at a private location.
Veronica believes the latest rape on campus is linked to a sorority house, so she attends a party there to gain information. Meanwhile, Keith runs for his life in the desert and Cormac pursues him. Back on campus, Logan and Wallace take part in a prison experiment for a class project in which Wallace plays one of the guards who needs to get information out of the prisoners, one of whom is Logan, within 48 hours.
The dean threatens to expel Veronica unless she tells him which faculty member supplied marijuana seeds to a sorority housemother; a jock's playbook is stolen and he believes it was taken to create an excuse to yank his scholarship; Weevil starts to work for Keith and goes out on his first assignment; Veronica worries that Logan is being unfaithful to her.
A necklace given to Veronica by Lilly Kane is stolen from her when two thieves break into an underground campus casino on Halloween night, and Veronica suspects Weevil is one of the robbers. Also, Dean O'Dell asks Keith to find his dying stepson's biological father before the boy dies so the child can say good-bye to him; and Wallace considers cheating on an exam after he learns he's failing mechanical engineering.
Logan believes his accountant is stealing money from his trust fund so he asks Veronica to investigate; Dick hires Veronica, on behalf of his fraternity, to prove that his fellow frat brothers aren't involved with the rapes on campus after an article in the school paper suggests there is a connection between the two; Keith becomes attracted to a woman who hires him to follow her husband and find out if he is cheating on her.
Veronica sets out to clear her name after she is accused by a student of plagiarizing a class paper she wrote. Her investigation leads to a surprising revelation. Also, Keith goes out with Harmony, and Veronica worries he's getting too involved with a married woman. Back on campus, Wallace is faced with a difficult decision whether to focus more time on academics or athletics, and Parker becomes attracted to Piz.
Veronica tries to find a missing student after the guy's out-of-town girlfriend shows up searching for him; Harmony asks Keith to go away with her on a romantic weekend, but he's afraid of what Veronica's reaction will be; Veronica attempts to get Mercer out of jail, but her efforts are thwarted when Logan refuses to say what Mercer's alibi is; Landry offers to help get Veronica an internship with the FBI.
A wealthy Hearst College trustee (Patricia Hearst), who will cast the deciding vote on whether to continue the Greek system on campus, disappears during a reception in her honor the night before she is to vote. Dean O'Dell quickly hires Keith to find her and Veronica helps out. Also, Logan fears for Veronica's safety since she was attacked and takes it upon himself to protect her.
Veronica is placed in danger when she discovers the identity of the campus rapist after attending a fraternity party. Also, Dean O'Dell suspects his wife is cheating on him, so he hires Keith to follow her; and Logan confronts Veronica about their strained relationship.
Veronica and Mac pose as members of an on-campus animal-rights group to search for a monkey missing from a research laboratory; Mindy asks Keith to investigate her husband's death because she believes he was murdered.
Veronica helps a student locate a woman he says he's in love with, but he doesn't know her last name or where she lives. He just knows she's getting married soon, due to a text message she sent to him. Veronica's probe reveals the mystery woman isn't all she claims to be. Also, Keith learns that Dean O'Dell's office was egged the night of his alleged suicide; and Madison stuns Veronica with some shocking news.
Veronica tries to find out who slipped a classmate a morning-after pill that caused her to have a miscarriage. During the investigation, Veronica learns there may be a witness to Dean O'Dell's death. Also, Veronica confronts Logan about sleeping with Madison while they were broken up.
Hearst's basketball coach is murdered and his widow (Tracey Needham) hires Keith to investigate and clear her son, who is Sheriff Lamb's chief suspect; Veronica learns that the alibis given by Mindy O'Dell and Professor Landry don't match; Logan gets stuck entertaining a 13-year-old girl when Dick invites friends over.
Josh claims he is being framed for his father's murder and asks Veronica for help. Meanwhile, Keith learns that Coach Barry's wife hired Vinnie Van Lowe to find out whether her husband was having an affair; and Logan joins Mac and Parker on a Valentine's Day scavenger hunt.
Keith arrests Professor Landry, during a class, for Dean O'Dell's murder, but Landry claims he is innocent. Meanwhile, Veronica catches Tim Foyle breaking into the offices of Mars Investigations; and Wallace becomes concerned when he spies Logan having an intimate lunch with Parker.
Veronica investigates when a restaurant owned by an Arab couple is vandalized and the word “terrorist” is spray painted on their door. Meanwhile, Keith cracks down on bars serving underage customers when a drunk 19-year-old man is hit by a car after leaving a bar near campus; and Logan invites Veronica to a birthday party for Parker.
A once-famous rock star (Paul Rudd) agrees to play a benefit concert at Hearst, but the gig is placed in jeopardy when someone steals music tapes from his hotel room. Piz, who is the musician's escort on campus, gets Veronica to take the case. Meanwhile, Logan hires Mac to help him create a Web site for a business-class project, and Keith investigates after getting a tip on a possible robbery attempt at a store.
Veronica is hired by a Ugandan native to investigate whether a Hearst student, who was forced by rebels to be a child soldier, is his son. Meanwhile, Parker is disappointed to learn that Logan is going away for the summer on a surfing trip with Dick; and Mac reconsiders her relationship with Max. At the sheriff's office, Keith investigates a string of home burglaries that threaten to derail his chances in the upcoming election.
Weevil hires Veronica after he is accused of making fake student debit cards and using them to commit fraud; Wallace is stalked by a male student; Piz interviews Keith and Vinnie about the upcoming sheriff's election on his radio show; and a sexy tape featuring Veronica and Piz pops up on the Internet.
The third season concludes with Veronica investigating the origin of a sex tape that features her with Piz. Veronica tries to keep Keith from finding out about the tape and she learns that a person from her past may be involved. Meanwhile, Parker confronts Logan about his feelings for Veronica, and Keith goes beyond the call of duty to protect his daughter.