Zack and Cody graduate from middle school. But while Cody has succeeded in school, Zack has done so poorly that he has to attend summer school, but is too scared to let his parents know.
After summer school, Zack takes a summer job working under Arwin, but finds the job so deplorable that he tries to get one at the local supermarket, even if it means working with Cody. The revelation that London can't swim, despite her on-the-side swimsuit business, forces her to take swimming lessons from Tipton lifeguard Lance, both of whom fall in love with each other. Little does she realize that the kids at Maddie's summer camp job are the ones she has to thank for this and other tabloid gossip, and even Maddie herself begins to see the benefits of their scheme.
Zack and Cody wish on a star and get super powers. Cody gets the power to read minds and move objects with his mind. Zack gets the ability to move fast. They find their arch-nemesis to be none other than Mr. Moseby, who plans to turn all children into small adults.
The manager of a rival Revolutionary War themed grocery store challenges Zack, Cody, and their boss to a speed-bagging competition. Mr. Moseby takes in his niece Nia, in order to smooth out her sassy attitude and short fuse. When it becomes clear that Maddie's replacement Millicent finds her job much too stressful, Moseby believes that a job at the candy-counter might be the perfect remedy... until she talks London into taking her to a concert and inviting the band, their crew, and their groupies over for a wild party.
Arwin's mother gets married, so Zach and Cody invite him to stay with them for a few days. Arwin quickly annoys the boys and Carey. Meanwhile, Lance breaks up with London.
It's Zack and Cody's First day of being Freshmans in High school and London's First day in public school. Everyone ends up being trouble for something on their first day.
The Tipton staff and London must attend a Team Building seminar, which doesn't go as planned. Meanwhile, Zack and Cody secretly let in a bug convention and let the bugs loose.
Cody accidently breaks up with his girlfriend Barbra when a rumor is spread that she is dating a handsome new violinist. London tries to take up the Tipton business by doing every job at the hotel.
When Zack and Cody's Dad move into town for a play, he buys an apartment room. Zack and Cody both bring their girlfriends to the apartment the same night.
London doesn't make the cheer-leading squad, so Cody helps out by forming a new cheer-leading squad with his misfit friends. Zack has his own problems on the basketball team.
The twins get grounded and are forbidden to leave the suite, leaving London's Internet show without a producer. Luckily, Maddie steps in and books Chris Brown as a guest star on the show. Meanwhile, Cody sneaks out and books some guest stars of his own, The Cheetah Girls.