Logan brings a present for the girls, a bear for the girls' lounge. Then people find out their secrets (i.e. Quinn eats baby food) and the girls start to blame each other for telling their secrets. And later trying to find out who is the culprit.

Prank Week, a PCA tradition where returning students prank new ones, has begun. The boys prank the girls multiple times, so the girls decide to prank the boys back (which violates tradition because new students are not supposed to do anything about it except getting pranked). The boys were supposed to keep a statue of the founder of PCA clean, so Zoey comes up with a prank and the girls put women's clothes on it. But when the son of PCA's founder sees it, he is very angry, and tells the girls that its going to be their last semester at PCA and that no more girls are going to PCA. So then after all the sadness from the girls, Zoey tries to figure out a way of how the girls can stay at PCA.

Zoey, Dana, Nicole sign up for the spring-fling committee in order to get Drake Bell to perform at their spring-fling. But when they find out they have to have $5,000 for Drake to play at spring-fling, Zoey and the gang put up a fund-raiser.

Chase and Michael start an online show, The Chase & Michael Show. Zoey and Logan have their own segment on it called "He Says, She Says" and it all goes wrong when all the boys and girls begin fighting, so Dean Rivers cancels their show. Meanwhile, Nicole is depressed because she is failing Algebra because of cute boys, so Quinn and Lola try to fix her problem by using a hypnotis technique.

After a fire burns down Sushi Rox, Zoey and the gang hold a people auction to raise money in order to rebuild it. Chase and Michael get auctioned to the sushi-crazy gym teacher. Zoey, Lola, and Nicole become Logan's personal cheerleaders, and they are told to "cheer his awesomeness", as in cheer for everything he does. His plan backfires when the girls decide to cheer for everything he does.

Quinn's pet alpaca, Otis, is depressed because he misses her, leaving her feeling depressed as well. The girls then decide to try and cheer her up by throwing an alpaca-themed party. However, this only made her miss Otis even more and she left PCA to meet with him, which could get her suspended as it is the middle of the semester. Meanwhile, the guys make a bet to see who can go the longest without saying anything containing the letter 'S' and the person who loses has to run across the campus wearing nothing but a bikini top, a hula skirt, and a flashing red helmet.

A new "hot" Dean fills in for Dean Rivers because Dustin,Quinn, and Dustin's friends hit Dean Rivers with a model airplane by mistake.. Meanwhile, the girls' Dorm Advisor Coco has just been dumped by her boyfriend, Carl. Zoey and her friends set up Dean Taylor and Coco on a date at Sushi Rox because Coco keeps complaining about Carl.

This time on Zoey 101, the Great Vince Blake appears to be the ladies' man, the best school athlete and the savior of the football team. He helped PCA advance to the state championships. Little do people know though, he is in fact a cheater as Chase catches him taking pictures of a history test with his cell phone. Chase must choose not to tell and let Vince cheat more or make PCA lose its biggest football game. Logan, Michael, and the football team convince him not to tell, but Zoey thinks he should. Meanwhile, Zoey, Lola, Quinn, and Mark put healthy snacks, called Moonbars, to try and persuade the students to stop eating junk food.

A science star named Paige considers attending PCA and is going to install her new energy converter to make PCA run on Paige-power. This upsets Quinn so she decides to rebel when she realizes that she may no longer be the smartest girl on campus and she gives up science. Meanwhile, Michael thinks he's going crazy, but it was a joke for a class project.

After a deceased relative of Zoey's sends her tons of boxes of ribs, Zoey, Chase, Micheal, and Logan agree to have a rib cook-off. After a fierce feud between Micheal and Logan, they decide to compete against each other with Zoey on Micheal's team, and Chase on Logan's. Quinn accidentally blows Mark's eyebrows off in an experiment gone awry.

Logan's father sends him a package from Japan, complete with a new Japanese cell phone and a horror movie. When Dustin watches the horror movie, he becomes so frightened that he has to start sleeping in Zoey's dorm room. Meanwhile, someone is pulling the fire alarm in the boys' dorm room and the boys set out to find the culprit. All the while, Michael does his best to coin a new phrase... "Drippin'."

Michael and Logan try to fool the housing lady into making a fake Chase in order to avoid getting a new roommate. Zoey accidentally gets Coco fired and tries to help her get her job back. Meanwhile, Dean Rivers hires Mira, the new dorm advisor. However, she has a problem: she steals everything that she sees. So, Dean Rivers fires Mira and Coco is hired again, but she isn't seen at the end of the show. Before leaving, Mira also steals Dean Rivers' car.

When the gangs' spring break trip to Yosemite National Park is canceled, they get to stay on PCA campus and have fun with no-one else around. However, Dean Rivers later accuses them of vandalism.

Much to Zoey's dismay, Dustin is Logan's new assistant. However, the job is short-lived after Logan leaves Dustin an angry voicemail. Soon, everybody hears the message, and learns about Logan and his temper. Dean Rivers sentences Logan to anger management classes. While Logan learns that he can get out of the classes if he can just keep his cool, Zoey is not about to let that happen . Meanwhile, Lola is disgusted and furious to learn that the peanuts she ate were from Peanut Lemon-Ms that Quinn had spat out.

Quinn and Mark agree to take a break from each other, but Quinn becomes upset when she later sees Mark with another girl. Meanwhile, a horse begins following Michael around campus.

The gang is surprised to find that former bully, Vince Blake is back at PCA. The girls decide to just ignore him, which is harder for some than others, but the guys think it's time for some revenge.

The Dean bans coffee carts on campus after an accident involving his wife, resulting in a war of the sexes when the girls and guys each try to come up with a scheme to circumvent the new rule.