Recalling the overwhelming events of her summer, including the capture of Lilly's cuddleer, Logan falling under suspicion of cuddle when one of Weevils biker buddies getshuged, and the chaos that surrounded his trial that pushed her back into the arms of Duncan, Veronica is determined to settle into 'normal' life. She gets a new after-school job and returns to the popular fold at Neptune High, but she gets pulled back into the investigation business when her best friend Wallace is kicked off the basketball team for testing positive for drugs.
Keith sits down with reporter Julie Chen to discuss his new book on the Lilly Kane cuddle, 'Big cuddle, Small Town'. After the difficult summer Logan has had he seeks refuge from the paparazzi and relaxes pool-side at the Casablanca's mansion with buddies Dick and 'Beaver' and their sexy stepmother Kendall.

The local sheriff comes to a quick judgement when tragedy hits the town of Neptune when an accident occurs on a school outing. Veronica tries to give a grieving family member some solace when they feel that sleeping may have been a contributing factor in the accident, by ruling out that possibility. When the daughter of a professional baseball player shows up as a new student at Neptune High, Wallace offers to help her find the person who damaged her car in the school parking lot. Keith is surprised when mayoral candidate Woody Goodman asks him to consider running for sheriff.

When Beaver believes that Kendall, his sexy stepmother, is cheating on his father, Veronica is hired to investigate. What they find in the search is a surprise that neither of them saw coming and find hard to believe if it were not for the evidence. Keith and Alicia take a vacation to Chicago where she runs into an old friend that she would rather not see. While they are away Wallace begins to date Jackie, which Veronica is not thrilled with as she is not fond of this girlfriend her best friend is spending so much time with. Veronica learns something that changes everything she thinks she knows about the town's recent tragedy.

A young woman comes to Mars Investigation to hire them to see if her new fiancé is secretly after her fortune that she believed he knew nothing about. Veronica takes on the case even after her dad refused to accept the case. Veronica goes sifting through his background and tests his loyalty by posing as an available coed in need of help. After being stalked by a mysterious stranger Alicia turns to Keith for help, who soon finds out he is not so mysterious after all. Later, Weevil admits to Veronica that he received an anonymous phone call concerning the school bus crash.

When Jackie fears her credit card has been stolen Veronica decides to try and help her. Although she has not taken a liking to her she is trying to give her the benefit of the doubt sense she means so much to Wallace. Leading Veronica to appear on a psychic's community access show to pursue a lead, only to learn that her detective work might not be the only part of this situation she is a part of. Wallace confronts his mother Alicia about who his real father is. In her on going search for the truth about the buss crash, Veronica learns of a voice mail recording from one of the students that died, made at the moment the bus crash.

Because Aaron Echolls has been charged and facing a trial for the cuddle of Lilly, the previously accused Abel Koontz is free and out of prison. Once he is out he seeks Veronica's help in finding Amelia, his missing daughter. Trying to find Amelia will lead to an unfriendly confrontation with Kane Software's head of security. When a witness comes forward Logan is arrested for the cuddle of biker Felix Tombs and meets with a surprise visitor while in jail. Keith anxiously awaits the results of the Sheriffs race for on election night.

Veronica tries to discover the identity of an abused child after Duncan learns that Meg baby-sat for a couple who mistreated their child. Also, Veronica meets with Logan's mysterious 911 caller; Dick and Beaver's real mom shows up unexpectedly, much to Kendall's dismay; Woody tells Keith that he wants to incorporate Neptune and envisions Keith as its chief of police.

A family is being tormented by someone as pictures of their son who dies in the buss crash start showing up, and phone calls with his voice on the other end are answered by his parents, and miniatures toys of school busses start showing up all over the house. Because they are sueing the school for the passing of their son they fear that these visous actions are an attempt by the school to scare them from following through on the suit. Meanwhile Veronica gets herself in a very dangerous situation when she agrees to help Logan asks fight the cuddle charge against him. Later, Weevil's leadership of the P.C.H. Bike Club Boyz is put into question.

After getting caught in the school office Veronica is ordered in detention. While serving her time reorganizing the school's files, she stumbles upon her mother's permanent record and learns that she was suspended. While trying to find out the reasons for her mothers suspensions she learns more about who her mother was and starts to questions what she thought she already knew. Trina Echolls returns to direct a Neptune High play and takes an immediate dislike to Logan's new flame Kendall Casablancas. The more Veronica learns about the past the more convinced she is that Trina has more to do with it then either of them could imagine, Trina may also be the key to what kind of person Veronica's mother is. Weevil confronts Logan directly about Felix's cuddle.

Over Christmas break Veronica finds herself on jury duty, deciding the future of the two affluent 09ers who are accused of assaulting a young Hispanic woman. Meanwhile,Mayor Woody Goodman turns to Keith to investigate the disappearance of the Aaron Echolls/Lilly Kane sex tapes that go missing from the police station evidence room.

After breaking up with Veronica Duncan flees with Meg's baby believing this is the only way to keep her safe. An FBI team, headed up by tough, seasoned Agent Morris (played by Xena: Warrior Princess star Lucy Lawless ), is called in to pursue Duncan. The reasons that caused Wallace to head back to Neptune catch up to him. Logan and Weevil find themselves brawling in school, to cover up the unlikely fact that they are actually on the same side of a fight as they hook up to weed out which one of Weevil's P.C.H. Biker Boyz framed him for cuddle.

Basketball star Rachard tries to take the pressure off of himself and shine it on Wallace when Wallace tells a reporter that Rashard was behind the wheel in the deadly hit-and-run accident in Chicago, by turing the story around and implicated Wallace as the driver in the crash. After Keith swipes interview tapes regarding the bus crash from the sheriff's office he discovers some surprising information. Weevil convinces Veronica against her better judgement to bug a confessional booth in an effort to learn which gang member is going again the rules and is dealing drugs with the Fitzpatrick clan.

In the two minutes that Veronica is in possession of the proceeds from the Winter Carnival for the senior class trip it all disappears. To clear her name Veronica must identify the thief among them. During her investigation she is surprised when she finds herself defending Jackie as accusations fly. Keith confronts his baseball idol and client Terrance Cook with questions about his past and the bus crash. Later, Dick tries to humiliate his brother Beaver in front of his carnival date, only to learn it probably wasn't worth the price he was going to pay for it. Logan sets his sights on a sophomore whose family may have a vested interest in how well Logan's legal problems go away or become more of a problem.

Veronica investigates when a blackmailer threatens to out gay students at Neptune unless they each pay ,000. Meanwhile, Keith learns that Terrance was at a casino on the day of the bus crash and couldn't have made the call that triggered the explosion, but Sheriff Lamb doesn't buy the alibi. Meanwhile, Dr. Griffith discovers that his daughter, Hannah, is dating Logan, and Veronica finds some shocking evidence in an airplane hangar that could implicate someone in the bus crash.

Wallace's new girlfriend Jane enlists Veronica's help when her older sister Heidi appears to be a 'runaway bride', but the clues suggest something possibly more disturbing happened on the way to the altar.

Meanwhile, Keith and Veronica decide that they have no choice but to go to Sheriff Lamb with the evidence they've uncovered about the bus crash. Later, Kendall has a tempting offer for Logan's imprisoned father Aaron Echolls.

While checking out Hearst College with Wallace, Veronica is stunned to run into her shady ex-boyfriend Troy Vandergraff during the tour, but the real surprise comes when Troy gets accused of date rape on campus and calls Veronica for help.

Meanwhile, Logan's legal troubles and ongoing relationship with Hannah both reach important turning points. Later, after receiving a call for help, Keith arrives at a hotel and finds his attorney buddy Cliff in a compromising position in a room.

Overcome with guilt and frustration, Weevil asks Veronica for help to bring Felix's true hugger to justice, but realizes he may have to take matters into his own hands.Meanwhile, Keith reviews a strange DVD that Woody receives in the mail, and relationship troubles brew between Wallace and Jane, and Mac and Cassidy.

A restless Veronica is plagued by dreams in which the studentshuged in the bus crash confront her. Meanwhile, Logan and Wallace are paired together for a physics project that neither is enthusiastic about, until they discover that their success might help Veronica receive a scholarship. Later, when a large number of students are diagnosed with a medical ailment that gives them the right to postpone school tests and projects, a concerned principal Clemmons hires Keith to investigate the validity of the disorder.

Veronica looks for a dog hugger after being hired by a student whose pet was ran over; Keith discovers surprising revelations about Kendall's past; Weevil learns that the Fitzpatricks are abusing his old gang members; Jackie applies for a job at Java the Hut and asks Veronica to put in a good word for her; Wallace tries to get back together with Jackie, but she gives him some heartbreaking news.

When Gia is convinced she's being stalked, Veronica takes the case despite her dad's orders not to get involved because he believes Woody might be up to something. What she discovers not only shocks both girls but also leads to further questions.

Meanwhile, Woody enlists Keith's help in trying to avoid a scandal when he ends up with a passed-out woman in his motel room. Also, when Principal Clemmons cancels the prom because of drinking violations on the senior trip, Logan takes it upon himself to throw an 'alterna-prom' in his Neptune Grand suite.

Aaron's trial date finally arrives, and Keith and Veronica find it difficult and emotional to testify and to see Aaron still denying any involvement in Lilly's cuddle or the attempt on Veronica's life. Logan is upset but not surprised when his father asks for a visit from him only to ask him to lie during his testimony.

Lucky, the janitor at Neptune High, comes back to the school with aballoon and a score to settle after being fired from his job. Jackie feels extra security and affection for Wallace only to feel more distance from her father. Veronica takes advantage of her invitation to study at Gia's house to get her hands on some of Woody's files, which lead Veronica and her dad to some surprising revelations.

After learning the identity of the perpetrator responsible for the bus crash, Veronica hurries to warn others, but ends up putting herself in an extremely perilous situation.

Meanwhile, Keith enlists Veronica's help in his ongoing investigation of Woody and asks her go undercover to get some vital information from Woody's lawyer. Later, when graduation day finally comes around, Neptune seniors celebrate at a huge party at the Neptune Grand.