Maddie Fitzpatrick visits the S.S. Tipton and gains a new friend in Bailey. Prince Jeffy of Linchtenstamp, who's only 8 years old, falls in love with Maddie and forces her to marry him. However, Zack challenges the Prince to a joust, with Maddie being the prize. Zack beats Prince Jeffy on a bouncing ball and using a water noodle weapon. Also, Zack finally gets his long-awaited kiss from Maddie.

Mr. Moseby announces that London's dad, Mr. Tipton is selling the ship and that it will be dismantled within a week.

The group starts rebuilding Kettlecorn after the tornado, but they continue to struggle to pay off the damage. As a result, London's father, Mr. Tipton arrives (who finally reveals himself) to discuss aiding their monetary costs. Meanwhile, Zack, Woody, and Mr. Moseby attempt to sneak into Kettlecorn with a Search and Rescue team.

After the students pull a prank on Mr. Moseby, he cancels the senior prom. So, Zack comes up with a plan to have a "secret prom". Meanwhile, Bailey tries to get everybody to vote her for prom queen while Cody helps Woody ask Addison to prom. Ultimately, the kids award the roles of king and queen to Mr. Moseby and Ms. Tutweiller.

Cody arrives in Kettlecorn and is surprised to see that Moose is also there to get Bailey back. A tornado approaches and everyone evacuates into the Pickett's storm shelter. As the tornado hits, Bailey is knocked out and dreams that she is Dorothy Gale and is trying to find her way back home through the Land of Oz. As Bailey unwittingly re-enacts the story of The Wonderful Wizard of Oz, she encounters Moose as the Scarecrow, Cody as the Tin Woodman, Woody as the Cowardly Lion, Zack as a Flying Monkey, London as Glinda the Good Witch and the Wicked Witch of the West, and Mr. Moseby as a Munchkin. She wakes up from her dream and has to decide between Moose and Cody.

While producing a news show for Ms. Tutweiller's class, each of the kids find their own set of problems. Zack and Bailey clash as co-anchors, Cody makes a shocking discovery linked to London during his investigative reporting, Kirby reminisces about the good ole days, while London is having trouble with the green screen.

Zack, London, Woody, and Maya are all trapped in London's shoe submarine with only enough air for thirty minutes. Meanwhile, Marcus helps Cody prepare to play chess against a beautiful Russian junior champion.

London's magic mirror takes her to a Christmas past, present and future, and realizes something which may change her forever.

When the new aqua lounge is flooded, Mr. Moseby vows to expel the student responsible for the mess. Although Mr. Moseby assumes Zack is the culprit, Cody, Bailey (who had just returned from Kettlecorn), and Woody all believe they are each responsible for the disaster for different reasons. Meanwhile, Marcus leaves the ship to make a Broadway musical based on his hit song "Retainer Baby."

When the ship is docked in New Orleans, Mr. Moseby tells the tale of the ghost of Captain Entenille, whose old steamship, the Jessie Belle, sunk 150 years ago. His spirit makes contact with Zack, sending him on a mission to prove the sinking of the old ship wasn't the captain's fault. Meanwhile, London and Bailey try to help Moseby overcome his fear of performing in public.

London offers to take Bailey to Kettlecorn to celebrate her grandmother's 90th birthday, but when their blimp malfunctions they are forced to drive the rest of the way. Elsewhere, Zack, Cody, and Woody challenge Mr. Moseby and his brother, who is visiting with his teammates, to a game of basketball, that is until they learn his brother is NBA star Dwight Howard. Meanwhile, Cody is unsure of where or why Bailey has gone to and laments her absence, until he discovers that she went to her family farm. He decides to go there to ultimately win her affections back.

Cody leaves the ship following his break up with Bailey to join an elite, non-religious, monk-like club which he hopes will help him get over the break up. Zack and Woody are determined to go there and save Cody. Meanwhile, London and Miss Tutweiller try to console Bailey by giving her relationship advice.

Maya's birthday is coming up and Zack decides to do something special for her. When singer Sean Kingston comes on board, he immediately becomes attracted to London. Zack misleads Sean Kingston into throwing a surprise party for London and also making Mr. Moseby believe it is for him, when it is actually a party for Maya. Meanwhile, Cody goes with Bailey to a Belgian chocolate factory on a couple's tour and runs into Woody who mistakenly came instead of attending a hiking trip.

Zack and Maya are officially together and she hopes he'll be able to attend her poetry reading on stage. The trouble is it's scheduled at the same time he, Cody, Woody, and Mr. Moseby are competing in an online war game for the championship against an Australian team. As a result, Zack splits his time between the two events. Meanwhile, for a community service project, London and Bailey run a daycare program for young children who seem to prefer London and Bailey doubts herself until trouble arises.

Cody shows Woody's sister around the ship. Meanwhile, London hires a double to do her chores, but she falls in love with Zack.

It's couples game night and the gang has a hard time finding a fun game everyone finds interesting. London tries to play a prank on Woody and it results in the release of a crate full of snakes. Meanwhile, Cody tries to prove he can be funny to Bailey and Zack tries to get forgiven by Maya when she learns how many girls he has dated.

After assigning the class to write their own play, Ms. Tutweiler selects Cody's play to be presented in class. However, Bailey refuses to participate after realizing the play antagonizes her role in the break-up between her and Cody, forcing Cody to act as Bailey and Zack as Cody.

Carey joins the boys while they're in Japan when she's selected to star in a soda commercial by a businessman who's taken a liking to her when he saw her perform at the Tipton. Shooting the commercial is difficult enough since the soda is flavored with shrimp and tastes awful. Things get worse when Zack smashes an expensive camera and the family has to pay for it by becoming tasters at the soda factory. Meanwhile, Woody is able to defeat a sumo wrestler in the ring to win an unlimited ship gold card. However, having lost his confidence, the wrestler continuously hangs around Woody, getting him annoyed to the point of facing him in the ring again in hopes he finally leaves the ship. Also, London does everything she can to avoid going to the dentist.

Cody goes to a scientific research facility in Antarctica, and Zack and Woody tag along to go snowmobiling. But after they arrive, the head scientist steals their snowmobile, stranding the boys at the facility, leaving them to find ways to survive until help arrives. Meanwhile, London's favorite fashion designer comes on board to announce he's quitting the business. She eventually tries to inspire him to find some new ideas for designs and come out of retirement.

London and Woody go to a posh beach club for senior ditch day, but when the bouncer won't let Woody in, London and Zack go without him. Meanwhile, in an effort to keep their perfect attendance records, Bailey and Cody show up for class, which annoys Ms. Tutweiller who was looking forward to her day off.

The Seven Seas High dance is coming up. Having broke up, Cody and Bailey lie about having dates to the dance, so they quickly try to find a backup date to backup their lie. Now the pressure is on to see who has the best game. Meanwhile, Woody is tired of Tutweiller and Moseby arguing about who should get the skydeck for the school dance, so he makes them share the skydeck. It is revealed though flashback that Mr. Moseby and Miss Tutweiler's interest in the Middle Ages and 1980s, respectively, comes from the tribulations they endured as outcasts in their youth. Through understanding, Mr. Moseby convinces Emma that they both have become successful adults and have overcome their painful pasts.

No longer a couple, Cody and Bailey must choose who keeps Buck, their pet rat. Kirby investigates both to see who will make the better owner, but Woody is bitten by Buck, creating a super-hero alter-ego "Ratman."

Zack becomes attracted to a girl named Maya, but when he realizes he is actually falling in love with her, he attempts to use the six month plan Cody devised to date Bailey. Meanwhile, Dante, the boy who stole Marcus's identity in Paris, stows away on board to have Marcus produce his next album. In addition, Cody is trying to condition himself to forget about Bailey by flicking a rubber band against his wrist every time he thinks about her while she is visiting her home in Kettlecorn.

Arwin comes on board the SS Tipton to improve the ship by adding a robot. However, problems start to occur when it begins to have feelings for Cody. Meanwhile, London and Woody enlist Zack's help to pass a gym class.

London, Zack, Cody and Mr. Moseby set sail on the S.S. Tipton for their semester at sea. London convinces her roomate to leave the ship so she can have a room to herself. Cody finds himself sharing a room with Woody, who is very messy, and Zack shares a room with Bailey, who is a neat freak. Nobody knows that Bailey is a girl who disguised herself as a boy in order to gain a position on the ship after she found that there were no more vacancies for girls. Zack and Cody agree to switch roommates, but Zack changes his mind after he finds out that Bailey is a girl. After everyone else eventually finds this out Bailey is allowed to stay, filling the position vacated by London's ex-roommate, and Bailey becomes London's new roommate. This is the last straw for London and she escapes to Parrot Island via helicopter.