Cody and Bailey fight to see who gets to keep their shared pet rat, Buck, and Kirby is picked to decide who gets him. Meanwhile, Woody believes he has gained special superpowers after being bitten by Buck.
After lying to each other about having dates, Cody and Bailey scramble to find dates before an upcoming dance. Mr. Moseby and Ms. Tutweiller face their unpleasant pasts when their personalities clash at the dance.
Zack, usually only into girls for their looks, takes a likeness to Maya, a new waitress at the juice bar, and tries what Cody did—exactly—to make Maya like him. Meanwhile, Marcus is forced to deal with Dante, the young singer who impersonated him, who wants to make a life for himself.
The Aqua Lounge floods, and Mr. Moseby tries to find the culprit, while everyone assumes they are the one responsible. The gang also says goodbye to Marcus, who leaves the ship to produce a Broadway musical of his hit song.
Sean Kingston boards the S.S. Tipton and Zack wants him to sing at Maya's birthday. Sean is in love with London, so Zack has to convince Sean that he's actually singing for London, not Maya. Zack also has to keep Mr. Moseby off his back, and tells him that it's his party, too. Cody goes on a romantic chocolate factory tour with Bailey, because they had tickets from before they had broken up.
When Zack promises Maya to be present at a poem convention, he is also invited to play in an important competition of a video game with Cody and Woody. How will he decide where he has to be? Meanwhile, London and Bailey work a day care center on board, and the kids like London better, which gets on Bailey's nerves.
Zack and Cody visit their mom, who is in Japan doing a new commercial; but the three are soon enslaved after Zack costs the company a substantial amount of money. Back on the ship, Woody accidentally gets involved in sumo wrestling and London is hiding from Mr. Moseby so she doesn't have to go to the dentist.
The ghost of a sunken ship haunts Zack, and he brings Cody and Woody along to recover the ghost's compass, which had been lost in the wreckage. Back on the ship, Mr. Moseby is afraid of playing piano in front of a crowd, despite his skill level, and Bailey and London want to help him do it.
Senior Skip Day, when all the seniors skip classes, approaches. Zack, London, and Woody go to a posh club, but Cody and Bailey show up (to Ms. Tutweiller's dismay), wanting to maintain their attendance records.
Cody goes out with Woody's sister after finding out she is beautiful, but things go downhill when he realizes just how much like Woody she really is. London, jealous of Zack, tries to find a twin (or rather, someone who is exactly like her) to do all the things she doesn't like doing.
When Arturo Vitali retires and visits the S.S. Tipton, London and Bailey try to help him find his muse again. Zack, Cody, and Woody become trapped in an Antarctican research facility with little food, water, or heat.
London and Bailey road trip to Kettlecorn for Bailey's grandmother's 90th birthday after London's blimp crashes. Back on the ship, Zack, Cody, and Woody are to play basketball against Mr. Moseby and his brother, until he finds out that he is in fact referring to NBA star Dwight Howard. Cody realizes that he wants Bailey back, and calls her, only to hear that she is in danger.
Cody arrives in Kettlecorn along with Bailey and London, just in time for ex-boyfriend Moose to arrive as well. As a tornado approaches, the Pickett family and their guests take refuge in the tornado shelter, forcing Cody and Bailey to work out their issues, lest Cody lose Bailey to her ex-boyfriend.
After the tornado passes, the Picketts find their home destroyed. London's father arrives, and the gang assumes he is there to help, until he announces he has purchased the land and zoned it for a plastic bag factory. After Zack, Woody, and Mr. Moseby arrive, Cody hatches a contrived plan to save the Picketts' farm.