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.

When the S.S. Tipton makes a special trip to pick up London from Parrot Island, Bailey, Moseby and Woody find themselves in jail because all the parrots left for Seal Island after Tipton Industries cut down all the trees. It's up to Zack and Cody to get them out of it but Zack and Cody end up in jail along with the others, and Bailey has to use her pig, Porkers, to rescue them. Zack and Cody fight for Bailey and Zack lets Cody have her after finding out about her ex-boyfriend Moose and seeing she has too much "baggage".

London and Bailey are on a mission to prove that Miss Tutweiller is dating Mr. Moseby after overhearing a conversation between the two. Meanwhile, Zack convinces Cody to sneak out after curfew to catch the Starlight Follies show on the ship. When they finally make it past the security guard and into the show, they become convinced that their teacher, Miss Tutweiller, is one of the showgirls by seeing her heart shaped anklet in the show, and during class, so Zack sends Bailey and London undercover as two showgirls to find out.

The ship is struck by lightning when it crosses the International Dateline, which places Cody in the same day over and over. He tries to use each day as a chance to let Bailey know how he feels about her, but something gets in the way every time. It's then up to Cody to divert the ship from the lightning to set them back on the right course.

The S.S. Tipton visits Greece. While they are there, Bailey crushes on the tour guide, which makes Cody jealous. To impress her, Arwin's cousin, Milos, gives him a replica of the ancient amulet of the Greek goddess Aphrodite to give as a gift to her, but in a mix up, he ends up getting the real one. Meanwhile, London has to write a speech for her father, who is funding a new exhibit, but finds it very difficult, but then has a dream about Greek history, which inspires her.

The class has a school project to complete and Cody chooses Bailey to be his partner, disappointing Zack who had hoped to get Cody to complete his and Woody's project for them. After Bailey tells London that she has partnered with Cody, London teams up with Zack and Woody. Cody is trying to catch a famous sea monster, but keeps failing and disappointing Bailey. Zack tries to sabotage Cody's project. However, his own project turns into a monster when London pours a smoothie into their plant project, causing it to grow and eventually trapping Zack, Woody, and London. The sea monster shows up at the end of the episode.

Chelsea, Barbara, and Bob visit the S.S Tipton. Cody is worried about how he's going to tell Barbara about his feelings for Bailey, but Barbara has to dump Cody because she and Bob are now dating. Right before Cody tells her about Bailey, Barbara tells him about her and Bob. To make Barbara jealous, Cody tells her that he and Bailey are also dating, thinking he can get away with the lie because Bailey is off the ship, but she returns early. London tells Chelsea that her room is her shoe closet, and that Woody is her servant. Woody agrees to help her because he has a crush on Chelsea. During movie night, Cody tries to make Barbara think that he and Bailey are dating, but Bailey eventually finds out. Cody apologizes and Bailey forgives him and says if he wanted her to be his pretend girlfriend, all he had to do is ask. To show it, she tickles him, wraps her arms around him, and finishes with a kiss on the cheek (causing Cody to faint) saying that would have made Barbara really jealous. Chelsea finds out that London is just a regular student, but instead of telling everyone, tells London she will tell everyone that London was "abducted by aliens" instead.

When Cody and Kirby don't allow Zack to bungee-jump off the side of the ship, the brothers accidentally knock Kirby off the ship, but Kirby lands in the hot tub. To make it up to him, Zack and Cody tutor Kirby so he can pass his high school equivalency exam to earn a better job. Meanwhile, London embarrasses Bailey on her internet show in a new segment called "Boo You!"

London holds a competition between Cody and Woody to decide which one of them will accompany her on her trip to the Tipton Space Station. Desperate to win, Cody and Woody each try to sabotage the other during the competition. Meanwhile, Zack is in charge of the senior citizen's activities and meets a passenger who is unwilling to participate in any of the activities. Zack makes multiple attempts to find something he wants to do and finally discovers that he enjoys playing pranks on other people. Together, they try to pull off a series of pranks on the other passengers.

Zack and Woody are convinced that a girl the S.S. Tipton rescued from the ocean is actually a mermaid. They make multiple attempts to prove it, but are unsuccessful. Upon her telling Zack that she is really a competitive swimmer and extremely busy training for the Olympics, Zack decides to teach her how to relax. Meanwhile, Cody is fired as the ship's towel boy after he doesn't allow passengers to use multiple towels in an attempt to protect the environment. He also puts up a show to portray the future of the Earth if this kind of overuse continues, which ultimately gets him re-hired as towel boy.

When Bailey starts feeling homesick, Cody decides to recreate her hometown festival. However, thanks to London, Bailey's hometown boyfriend, Moose, shows up. He and Cody compete in corn bobbin', arm wrestling, and chess to win Bailey's heart, but Cody loses every competition. Moose asks Bailey to come home, so she asks Cody what to do. Cody says to follow her heart and Bailey stays because she would miss her friends

Hannah Montana boards the S.S. Tipton on her way to a concert performance in Honolulu. To impress Bailey, Cody desperately tries to get tickets to the show. Meanwhile, the Russo's are still aboard the ship on their vacation in which Alex pulls a prank on Justin by putting blue dye in the hot tub, making him turn blue, for which Mr. Moseby blames Zack, while Max tries to impress London with his magical suitcase.

The crossover starts on Wizards of Waverly Place S02E25 Cast-Away (To Another Show) (I). It continues on Hannah Montana S03E20 Super(stitious) Girl (III).

London wants to become the assistant to the ship's magician after she develops a crush on him. Meanwhile, Zack wants to spend more time with Woody.

As punishment for setting off a stink cloud, Zack is made hall monitor, a role which he takes way too seriously. After sending half of the school to detention, Zack experiences the repercussions of upsetting all of his friends. Meanwhile, Bailey gets a job at London's boutique, an extension of London's personal closet.

Bailey gets jealous when Cody gets attention from other girls after he becomes the substitute home-ec teacher. Meanwhile, London tries to sell Zack's "paintings" which are things he's had in his mouth when he sneezed.

After Bailey and Cody try to get London to be smart for a bet, London becomes smart from a perfume. Meanwhile, Zack's prank for Woody goes awry when it accidently gets pulled on a female wrestler.

When Zack turns in one of Cody's old essays as his own, Ms. Tutweiller thinks he has a fear of bananas. Meanwhile, London goes through withdrawal when her cell phones are taken away in class.

Shortly after the start of a new semester on the ship, Zack, Cody, London, Bailey, and Woody are all cast-away on a life boat London was using as a closet and eventually find their way onto a deserted island. Cody's relationship with Bailey starts falling apart after an argument over wind patterns emerges and causes a fall out with the remainder of the group. Back on deck, Ms. Tutwieller and Mr. Moseby are put in exactly the same predicament as the others and even have the same disagreement over control of the operations. Cody and Bailey mend their relationship at the end of the episode.

Zack is surprised to learn that he has a new roommate who used to be a famous rapper until he hit puberty and his voice got deep.

Zack and Cody receive a $200 check from their parents for their 16th Birthday, but have an argument about how to spend it. During the argument, they both wish they were an only child and once the ship enters the Bermuda Triangle, their wish comes true.

Zack, Marcus, and Woody create a fake beauty pageant so they can meet girls. When Mr. Moseby learns of their plans, he punishes them by forcing them to see it through. Meanwhile, Bailey enters the pageant to try to beat London and hires Cody as her coach, but gets mad at him when he becomes too controlling.

After Mr. Moseby forbids the gang from playing football, they become interested in fantasy football.

Cody tries to find out who stole a valuable book.

The gang all have dreams of being characters in three different fairy tales; Hansel and Gretel, Snow White, and Jack and the Beanstalk.

A class assignment requires the students to simulate marriage to learn the challenges that face married couples in everyday life. Cody 'marries' Bailey, Zack 'marries' London, and Woody 'marries' Addison. However, when the "Wheel of Life" gives Cody as injury, he and Bailey begin to fight.

When Mr. Moseby leaves to go to a reunion, Zack and Marcus decide to throw a party on the sky deck with models. Janice and Jessica, from the Boston Tipton, come aboard the ship as models and while Janice tries to draw Zack's attention, Cody believes Bailey is jealous of Jessica. Meanwhile, to distract the modeling agent from discovering the party, Woody pretends to be a male model named Woodlander.

Cody wants to buy earrings for Bailey, but Zack insists he bargain with the cashier for a better price. Meanwhile, London, Bailey, Marcus, and Woody discover a magic lamp that contains a genie willing to grant wishes, causing them to argue over which wishes should be granted.

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.

Centuries in the future, Starship Tipton resident prankster Zerk (Zack's great-great-great-great-great grandson) plays a joke on feuding aliens and because of it, they vow to destroy the starship. The kids must travel to the future to save their descendants and fix the problem before it's too late. Meanwhile, London discovers that she has a great-great-great-great-great grandson, Rome, and that the Starship Tipton belongs to her family.

Cody and Bailey are planning to celebrate their one year anniversary when the SS Tipton docks in Paris. Cody asks London to help him make his date perfect. However, a big misunderstanding begins when Bailey sees Cody with London (who were just practicing the date) and mistakes her as the "hideous French girl". The next day, the day of the anniversary, Cody sees Bailey with another guy, Jean Luc, who was just trying to cheer her up. Bailey and Cody start arguing about the misunderstanding, and decide it would be better if they broke up. Meanwhile, Zack and Woody are pursued by art thieves.

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.

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."

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.

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.

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.

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."

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.

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.

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.

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 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.

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

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.

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.

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 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.

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.

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 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.

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