Pacific Coast Academy, an all boys boarding school is accepting female students for the first time since the school was established. Zoey's little brother Dustin is currently a student there. Zoey decides to be one of the first girls to become a student at PCA. This is very exciting, but also very scary; fitting in at a new school is hard enough, but going away to boarding school and living on your own at age 13 can get crazy! Especially when the girls are heavily outnumbered by the boys...
Zoey returns to PCA, hoping to tell Chase how she feels about him, but her friends have shocking news to tell her: Chase has recently moved away from PCA to find her. After Chase and Zoey get to meet, they agree to go on a "video chat date". Even with Zoey's communications problems and Chase's obnoxious roommate,Colin. Chase manages to tell Zoey "I love you". Zoey agrees too by returning Chase her own love. However, they wait due to the problems of having a long-distance relationship and decide to move on until Chase moves back to PCA so they can be together. Guest Star: Sean Flynn
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.
A new guy moves into Chase's room and catches Zoey's eye. Rumors begin to go around that Zoey has a crush on him.
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.
Zoey is running The Big Walk, a charity walk-a-thon at PCA, and everyone is getting sponsors to donate. When Lola pledges more money than she can handle, only Zoey can help her. But after visiting the scary head of the charity organization, Zoey breaks it to Lola that they need to come up with the missing money or else. Meanwhile, Quinn and Logan are beginning to realize that they don't hate each other. But when Michael may have seen too much, they have to make sure that he and everyone else knows just how much they still dislike each other.
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.
Zoey and James are finding it difficult to get some time alone. Zoey wants to go on a date with just James and none of their friends. Meanwhile, Logan and Quinn are tired of all of the sneaking around, and they plan a romantic dinner. Both couples, however, find their plans backfiring in unexpected ways as their night gets a little too crowded.
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.
Zoey's Physics teacher decides to take the class on a field trip to go on a roller coaster, and all the students are ecstatic, except for Michael. He's got a big problem, but will the gang be able to help him out, and will Lisa stand by his side?
The end of the school year is approaching, and that means Prom is too! Zoey is going to spend her summer in Maui, but when James offers to come along, her reaction isn't what he expected. Quinn and Logan want to go to prom, but they want to keep their secret safe too, so they decide to pick each other's dates -- the result is not what either of them expected. Meanwhile, Lola is made head of prom committee, and all she wants is to arrive fashionably late, but will she be able to?