The season continues the story of Veronica Mars, now a freshman studying at Hearst College while moonlighting as a private investigator under the wing of her detective father.
Veronica begins college with Logan, Wallace and Mac, but is immediately drawn back into old detective habits when Piz, Wallace's new roommate, gets all his stuff stolen. Meanwhile, Keith helps reunite Kendall with an old love, recently released from prison.
The campus newspaper hires Veronica for an undercover expose on the Zeta Theta sorority sisters during rush week to investigate Parker’s rape. Veronica begins to realize though that not everything is as it appears in the sorority house. Logan and Wallace take part in a challenging Sociology class role-playing experiment as prisoner and prison guard, and Keith treks through the desert after escaping from the scene of a crime.
Veronica's detective prowess is again used on campus when Piz's football friend loses the team playbook and Veronica must get it back before the game. The Dean threatens to expel Veronica if she doesn't reveal the source of her newspaper article. Meanwhile, Keith hires Weevil to work in the office, and Logan's antics catch up with him.
Logan gets a big surprise when he hires Veronica to find the source of his missing inheritance, which escalates from weird to worse. Meanwhile, Dick's fraternity asks Veronica to prove their innocence in the campus rapes, and Keith helps an old acquaintance prove her husband is cheating.
When the illegal casino Veronica frequents is robbed, she must track down the thief to recover the necklace Lilly gave her years before. Meanwhile, Dean O'Dell's stepson is dying of cancer and needs Keith to track down his biological father for a transplant (with Cliff's help), and Wallace fears he may flunk out of his most important class.
When Veronica's term paper appears on the internet, she is accused of cheating by the TA and must prove her innocence. Meanwhile, Wallace has problems of his own when long basketball practices distract him from his studies, and Keith begins seeing Harmony Chase.
Veronica helps a girl named Meryl who is certain that her boyfriend is in trouble, while a jaded Veronica tries to convince her that he is cheating. Meanwhile, Logan reluctantly tells Veronica why he is sure Mercer didn't commit the rapes, and Keith finds that there is a heavy price to pay for committing adultery.
Keith and Veronica are hired to help find the missing grand-daughter of the founder of Hearst College, whose swing vote could spell the end of fraternities and sororities at Hearst. Meanwhile, Logan fears for Veronica's safety as she gets closer to the truth regarding the campus rapes.
After the campus rapist anonymously announces the location of his next rape, Veronica hires her friends to help her track him down, but is shocked when she discovers the rapist's identity. Meanwhile, Logan makes a drastic decision about his future with Veronica, and Dean O'Dell hires Keith to prove that his wife is unfaithful.
Veronica and Mac help campus researchers locate a missing monkey who was allegedly stolen by animal rights activists. Meanwhile, Keith is approached by Mindy O'Dell, who claims her husband's death was murder, not suicide. And in the aftermath of his breakup with Veronica, Logan turns to Dick for advice.
Veronica is hired to track down a one-night-stand, but the situation becomes more complicated when she turns out to be a hooker. Meanwhile, Keith continues his investigation in Dean O'Dell's death, and a visit by Madison Sinclair causes trouble for Veronica and Logan.
Veronica is hired to find out who slipped a classmate a drug causing her to have a miscarriage against her will, but is distracted by Logan who admits to sleeping with Madison Sinclair. Meanwhile, Keith helps Mindy O'Dell when her ex-husband breaks into their house.
Keith takes on a second concurrent murder case when the head of the Hearst basketball team turns up dead and his son is the prime suspect. Meanwhile, a depressed Logan refuses to leave his hotel room and ends up babysitting Dick's girlfriend's little sister for days.
When Veronica is released from jail, she is contacted by Josh Barry who is desperate to prove his innocence in his father's murder. Meanwhile, Keith gets bittersweet news from the county commissioner, and Logan helps Mac and Parker on a scavenger hunt.
When Veronica discovers Timothy Foyle breaking into Mars Investigations, she uses his help to track down Dean O'Dell's true killer. Meanwhile, Logan and Parker's relationship takes an unexpected turn, and acting Sheriff Mars brings another murderer to justice.
With Keith acting-sheriff, Veronica goes solo on a case involving a local restaurant whose owners are the targets of hate crimes. Meanwhile, Keith is disturbed by the lack of professionalism in his deputies when he orders them to fine bars serving alcohol to underage patrons. Logan throws a birthday party for Parker, and Piz decides to finally confront Veronica about his feelings.
Desmond Fellows, a singer/musician from a 1990's pop band arrives on the Hearst campus to perform at a benefit concert to keep the station from going out of business. Piz gets the job of his dreams when he is put in charge of hosting Fellows around campus and on air. However his dreams start to dissolve as things don't go quite how he imagined, in more ways then one. Keith is excited about the upcoming Sheriff's race unopposed until he unwittingly helps promote an unlikely candidate who throws his hat into the ring.
Apollo, a Hearst student who suffered hardships as a child soldier in Africa, appears on Piz's radio show, prompting a man to come forth claiming to be his father. But Veronica's investigation unearths some surprises. Meanwhile, Neptune is faced with a crime spree that could spell trouble for Keith's campaign, and Logan finds himself in a difficult situation when Parker wants to spend to summer with him. Veronica awaits the results of her FBI exam.
Weevil asks Veronica to clear his name after he's arrested for selling fake debit cards to Hearst students, claiming he's being framed because of his criminal background.
As the end of the first semester at Hearst College draws to an end, the election for sheriff in Neptune comes to a close and Veronica and Piz discuss the effect a summer apart will have on their relationship.
