The district attorney's office tries to discern who is responsible for Trey's shooting. Julie and Jimmy team up to protect Marissa. Julie visits Trey in the hospital after he wakes from a coma and tells him to point the finger at his brother. Kirsten finds a friend who is also battling alcoholism. Trey recants his testimony after a visit from Marissa and then sets off out of town.
A petition circulates among the Harbor School parents to expel Marissa and Ryan because of the shooting and Dr. Kim brings in a new Dean of Discipline to handle the matter.
Marissa and Ryan's parents try to keep them apart, but they can't stop the two. In fact, Marissa and Ryan share their most intimate moment ever. Seth and Summer try to work Marissa and Ryan back into Harbor after their own interaction with Dean Hess. Caleb's will is finally read. Jimmy gets beat up for his unpaid debt. Kirsten finally returns home.
Marissa has to adjust to going to a new school (Newport Union), but her reputation has preceded her. New news about Taylor Townsend may even the playing field between Seth, Summer and Dean Hess. Charlotte arrives in the O.C. Julie Cooper tries to handle the fact that Caleb left nothing.
Summer and Seth try to out Hess's secret romance with Taylor. Marissa seeks help with Ryan from her public school colleagues. Ryan decides to go to work as a fisherman. Charlotte targets Julie for her plan. Sandy confronts Hess with knowledge of his trist with Taylor and demands that he re-admit Ryan.
Taylor Townsend organizes a school lock-in for the whole senior class. Marissa's new schoolmates celebrate the arrival of good waves. Marissa misses a Cohen family event due to spending time with Johnny. Johnny catches his girlfriend cheating on him at a party.
Taylor's interactions with Seth causes friction between Seth and Summer. Marissa tries to keep things from boiling over between Ryan and Volchok.
Ryan, Seth, Summer and Marissa weigh their future plans as Harbor students prepare for college as applications become due. Taylor confronts Summer with news that Seth has plans to go to college on the East coast.
Ryan's internship becomes odd when Matt takes Ryan to a strip club. Summer and Seth attempt to assure their entry to Brown University by becoming stand-out students and begin to compete when Summer's fantastic SAT results reveal a hidden intelligence. Johnny and Marissa continue to get closer as Marissa secures a meeting with a doctor for him. Julie and Kirsten start a party planning business.
The gang comes together for another Chrismukkah and Seth suggests that Ryan have a Bar Mitzvah to raise money for Johnny's surgery. Johnny nearly tries to make an armed robbery, but Ryan stops him and convinces him to "let the rich people help".
Ryan, Summer and Seth try to get Marissa back into Harbor. Johnny tries to come to turn with his feelings.
Kaitlin Cooper returns from boarding school for break which means Julie has to explain everything that's happened in her absence, but Kaitlin comes home with problems of her own.
Marissa prepares for Kaitlin's fifteenth birthday. Summer and Seth both get interviews for Brown. Johnny tries to hide his relations with Kaitlin, but she has other ideas.
Seth continues to lie to Summer about the Brown interview. Ryan confronts Marissa about her feelings for Johnny. Julie decides to set up Summer's father for the matchmaking service in the hope that he'll realize she's the one for him. Julie's attempt at spying on Dr. Roberts' date backfires. Summer finds Seth's pot stash. Ryan and Marissa race to help a drunk Johnny after Kaitlin calls asking for help.
Valentine's Day hits the O.C. like a ton of bricks in light of Johnny's fall from the oceanside cliffs and subsequent death. Everyone celebrates Johnny's life with a goodbye on the beach. Seth and Sandy accidentally switch Valentine's gifts.
Ryan and Sadie find a way to reconnect when the two make a stop in Ryan's former neighborhood during a trip to see Johnny's family. Meanwhile, Seth and Summer discover the truth about Julie and Dr. Roberts, while Marissa is linked to Johnny's death.
Sandy intervenes when Ryan decides not to invite the estranged Marissa to his big 18th birthday bash. Meanwhile, Marissa and Summer come clean to Julie and Neil.
Ryan's relationship with Sadie is strained when a longtime friend comes back to town and seeks his help. Seth and Summer also try to deal with a problem of their own. Meanwhile, Marissa copes with her current single status, while Sandy's Newport Group is flooded with obligations to be tended to.
Julie and Dr. Roberts spread the news of their engagement. Marissa and Julie end up as houseguests as Summer's place, and Marissa begins to hang out with Volchok's rough-and-tumble crowd. Meanwhile, Seth continues to worry about Marissa, putting a damper on Ryan's burgeoning romance with Sadie, though Kirsten has a plan to show Seth a fun time.
The kids receive their college acceptance and rejection letters, forcing them to make some life-altering decisions. Ryan and Sadie try to decide what do after high school and their decision concerns Sandy and Kirsten. Taylor throws a College Sweatshirt Party at Harbor and Marissa and Summer patch up their friendship. Meanwhile, the drama surrounding Sandy's job intensifies and seeps into the Cohen household.
While visiting his mother, Ryan has an experience with one of her coworkers. Due to Seth being so secretive, Taylor and Summer decide to come up with a plan to find out what his deal is.
With Graduation around the corner, the O.C kids are off to visit colleges. While on his visit to Brown, Seth runs into Anna, sparks fly and could very well bring an end to his relationship with Summer. Meanwhile, Kristin seems to be falling back into old habits after seeing Theresa and her baby boy at the airport.
There seems to be a lot of excitement on prom night. Ryan has arrived with a new flame while Summer's night becomes a complete bust, Marissa and Volchok decide to go together while Taylor’s money seems to be missing. In the end, one of the girls will be named queen and things truly come together for the bunch.
Ryan and Volchok make a deal after a fallout at prom. Sandy is chosen as Man of the Year, but this sparks the DA to dig deeper into his involvement with the hospital problems. Marissa goes and sees Kaitlin at her boarding school and Seth visits the Newport Group HQ and lights up the joint.
It is graduation day for Ryan, Seth, Summer, and Marissa at Harbor High School. After graduation they all went out to eat and celebrate their graduation.