When Cody rooms with Woody, the two conflict personalities and things get hectic. Though Bailey originally disguised as a boy to sneak aboard, her identity is revealed and she is bunked with London, who forced her roommate to quit school.
The gang heads to Parrot Island, where London escaped to after being forced to bunk with Bailey. Though they are jailed for being connected to the Tipton organization, will London, Mr. Moseby, Cody, Zack, Woody, and Bailey be able to escape in time to catch the boat before it leaves port?
After Zack spends all of his and Cody's money on partying, the two are forced to get jobs. When Cody spies an upcoming yo-yo contest, he decides to enter for a chance at the $1,000 prize. Meanwhile, Bailey is sick of London taking all the space in their cabin, so she invents a story to scare London.
Arwin's cousin, Milos, is employed at the ship's next destination, a posh Greek museum. When he accidentally gives out a real necklace instead of a replica, Zack, Cody, and Bailey must help replace the true one before the museum owner finds out.
Chelsea, Barbara, and Bob of The Suite Life of Zack & Cody board the S.S. Tipton. Cody is worried about having to dump Barbara, but is even more worried when he finds out she's dating Bob. Meanwhile, London has to convince Chelsea that she is the most pampered student on the boat.
After a freak accident, Zack and Cody try to make it up to Kirby by helping him pass his high school equivalency test. London tries to embarrass Bailey in public, until she finds out just how much it hurts.
When Cody and Zack visit an old Swami in India, they find out that he is just an entrepreneur in it for the money. All the while, Padma has returned and needs London to pretend she's actually her roommate.
When Maddie comes onto the S.S. Tipton for a short vacation, Zack does everything he can to win her heart after she takes to a prince. However, Zack really has to help her, once she finds out that the prince isn't all she hoped he would be.
The ship docks in Rome and Cody drags Zack to a famous restaurant. But when the staff quits, Cody and Zack have to fill in. London falls for a boy named Luca, until she finds out he is a con man. Then Mr. Moseby and Bailey must help her get a wad of cash back that she gave to the boy.
London and Bailey go to a hypnotist's show and London suddenly starts acting like Bailey, much to Bailey's chagrin. Meanwhile, the Harvard Dean is on board, and Cody wants to do everything he can to impress him—until his daughter wants to date Zack, who is recognized by the Dean as the resident clown.
When Zack and Cody's parents are offered full-time contracts on board the S.S. Tipton, they must hatch a plan to keep their parents from harassing them every day. London tries everything she can to find the perfect birthday gift for Mr. Moseby.
While Zack takes charge of the senior's part of the cruise and has to deal with a particularly grumpy old man, Cody and Woody are being tested by London to see who will accompany her to the Tipton's space station. But will she even pick one of them?
A girl, Marissa, is found at sea and brought aboard the S.S. Tipton. Zack and Woody are convinced she's a mermaid, but when Zack finds out she's actually a professional swimmer, he becomes great friends with her. All the while, Cody is fired after he preaches environmental conservation as the ship's towel boy.
When a secret microchip containing sensitive information is stolen by a woman who appears to be an assassin, a would-be spy attempts to use Zack and Cody to recover it. But when Cody tells Bailey, she wonders if she can trust him.
After a magic show, London takes after the magician, and Zack tries to hang out with Cody and Bailey, which interferes with their relationship. Desperate, they get Woody to take Zack off their hands for an upcoming music contest.
After Zack's misbehavior gets out of control, he is assigned to be a hall monitor. But he carries things a little too far, and things start to get out of hand. This doesn't help Cody and Bailey, who are trying to find more time to see each other; but with Zack on the prowl and Bailey getting a job, they begin to get separated.
When Cody fills in for an injured Home Economics teacher, the girls in the class fall for him, infuriating Bailey. Zack accidentally sneezes on a canvas, and when London tries to hand it in for art class, she accidentally finds someone who wishes to buy it for $30,000—but neglects to cut Zack in.
To win a bet against Cody, Bailey tells London that she has a perfume that makes her smarter. She gets a C on her next test, and begins to do well, until she finds out it's all a scam. With the final coming up, Bailey has to find some way to get London to study again. Meanwhile, the captain of the female wrestling team takes after Zack, and he attempts to get away from her, constantly afraid that she can beat him up.
Cody makes a "Missing You" video for Bailey while she's visiting London's grandmother in Thailand, but is dragged away by Zack who scores a double date. In Thailand, London is trying to make her grandmother more modern, despite her insisting that she is happy as-is.
After Zack steals one of Cody's old papers, Ms. Tutweiller is worried that Zack may have a serious phobia of bananas, and forces him to see the ship's counselor. London's phone is taken away in class, and she has to learn to live without texting for a week. Meanwhile, Woody has become addicted to a game called Better Life, and Cody tries to help him quit.
After a new semester begins, Zack, Cody, Woody, Bailey, and London are all aboard a life raft when it departs from the S.S. Tipton, and floats adrift into the sea. Cody and Bailey argue over who's better at everything, and London goes nuts, thinking she is in a plush hotel, and Bailey helps her to fulfill her hallucinations. Back on the ship, Mr. Moseby and Ms. Tutweiller realize that the students are missing, and go try to find them—getting themselves marooned as well.
Marcus Little, a famous singer who has left his stardom behind, comes on board and is bunked with Zack, who is sure he has seen Marcus before. Cody tries to impress Bailey at a series of games, but Bailey constantly emerges victorious, even in things she has never done before.
The week's guest singer, Jordin Sparks, comes aboard. Cody, Zack, and Marcus try to write her a song, but are more concerned with becoming a hit than producing something she would want to sing. Meanwhile, London hosts a "friend-for-a-week" contest, and the winner steals her identity.
After Zack, Marcus, and Woody create a fake beauty pageant to meet cute girls, Mr. Moseby discovers this and makes them actually set up the pageant. Bailey wants to show London up, and enters the pageant with Cody as her coach.
Zack and Cody travel to Martensgrav, a Swedish town that was founded by their ancestors Knuut and Olaf. But they soon find out that their ancestors are falsely thought to have nearly destroyed the town, and set out to clear their name.
Esteban of the Tipton Hotel comes on board to get married, and the boys try to help him relax and party a bit first. But things may be going slippery when Esteban's mother disapproves of the wedding—can Bailey and London convince her to allow it?
After Cody forgets to do his homework, he invents a series of tall tales to buy him more time. During the panic he's caused, Zack and Mr. Moseby are handcuffed together, and have to experience each other's lives.
London joins a fantasy football league created by Zack, Marcus, and Woody, and brings her own deal to the table—Kurt Warner. Cody, however, isn't very good at football and wants to improve, so he hires Kirby to help him out.
Cody, a member of a Sherlock Holmes club in Boston, drags Bailey and Woody along to the Sherlock Holmes museum, only to have to solve a real crime—when a rare book belonging to the queen goes missing. Just outside, Zack and Marcus must play a perfect game of croquet after accidentally challenging a pair of champions.
London offers a million dollars to whoever can come up with the best idea for her dad's new business, and Zack, Cody, Bailey, Marcus, and Mr. Moseby all come up with ideas to present to her. But will they get their prize after Kirby loses the money in safekeeping?
When the class is grouped into pairs to simulate marriage, Cody and Bailey break up, London spoils Zack, and Woody and Addison learn what it's like to have children, which sends the entire class for a loop.
Zack and Marcus host a models' competition on the sky deck, and Jessica and Janice show up to participate, making Cody believe that Bailey is jealous of the gorgeous twins. Woody, on the other hand, has to dress up as a model to keep the models' agent from discovering the "competition".
Zack tries to help Cody buy a pair of earrings for Bailey that he believes are one-of-a-kind. Back on the ship, London beings forth a magical lamp with a genie; London, Bailey, Woody, and Marcus try to decide who gets the wishes.
Cody and Bailey lock themselves in the engine room, along with Zack and Woody and turn off the ship's engines after they learn that a group of endangered whales is in their path. Can they hold out long enough when Kirby and Mr. Moseby trying to get things fixed?
Ms. Tutweiller's class is assigned to broadcast news that will be seen on board by the passengers of the S.S. Tipton. Zack competes with Bailey as co-anchors, Cody's a field reporter, and London's on weather.
The ships docks in Paris, and Bailey enjoys the company of a young and gorgeous painting prodigy. When Cody sees this, he immediately becomes jealous, but wants to ask Bailey what she's doing. But when she finds London in his arms during a practice date, the two have it out and break up.
Meanwhile, Zack and Woody are being chased by art thieves, and Marcus's identity is stolen by a boy named Dante.
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.