Starting a new school year, this time aboard the S.S. Tipton going to the Seven Seas High School, the twins are looking forward to getting new friends, while also visiting famous places worldwide where the boat will dock. However, London is less than satisfied at the school and does whatever she can do to escape.
London finds a way to escape her living nightmare of Seven Seas High, giving Bailey a bad conscience that she may have had something to do with it. Meanwhile, the boat takes an unexpected stop at Parrot Island to find London, but when the whole gang is arrested, they may not get back to the boat in time before it leaves.
Cody enters a Yo-Yo trick competition to win the prize money and hopefully Bailey's heart, but his attempt is shattered when it turns out another contestant is a much better player than he is. Meanwhile, Zack uses his student cards to shower all the girls aboard the shop with lots of presents, but when he maxes out his and Cody's cards, they need to find other ways to get food.
In a parody of the classic tale of love portrayed in "Titanic", Zack falls in love with a smart, sophisticated woman who boards the ship with her boyfriend. However, when her boyfriend's jealousy causes him to frame Zack for stealing a valuable necklace, the friendship between Zack and the beautiful woman may be broken. Meanwhile, Cody becomes the referee of a competition between London's pet dog and Bailey's pet pig, in which the losing pet must swim home.
Zack and Cody sneak out of their rooms after curfew to see a show featuring showgirls, but they get in trouble trying to enter the show and wind up getting help from Woody and London. Meanwhile, London and Bailey believe Mr. Moseby and Ms. Tutweiller are dating, so they follow them in secrecy and tries to prove the twin's wrong, who think they're not dating.
As the boat is about to cross the International Dateline, in which strange things often occure, Cody uses the opportunity of a school dance to get closer to Bailey, maybe even developing more than a friendship. However, when the boat crosses the Dateline just as Cody makes his move, time is reversed and the day is repeated. What will make the day stop repeating and will Cody manage to develop a relationship with Bailey?
The boat docks in Greece so that the students can take a visit to the new museum sponsored by London's father, but London has gotten the assignment to write a speech, so Ms. Tutweiller attempts to guide her through the process. Meanwhile, Cody buys Bailey a necklace from the museum's gift shop, but when it turns out the gift he gave was the real necklace and not a copy, the twins with Bailey now need to sneak into the museum and swap the necklaces while London is giving her speech.
Much to Zack and Woody's disgust, Cody and Bailey decide to pair up to create their science project, which is finding evidence that Galapagos Gurtle exists. However, when they stay up all night just waiting for a single trace, they start fighting so much their friendship may be destroyed. Meanwhile, Zack and Woody pair up with London to create their own project, but by accident, they create a sea monster which takes them hostage.
The gang is visited by old friends when Cody's girlfriend Barbara, Zack's friend Bob and London's rich friend Chelsea board the ship. While Zack wants to spend some real guy time with Bob (as he thinks Cody is boring and girly), Cody worries about how he should break up with Barbara, as he is in love with Bailey. However, in secrecy, Bob and Barbara are a couple and Barbara is stressing about how to break up with Cody. Meanwhile, London tries to cover up all aspects of living like normal students throughout Chelsea's stay, but it gets harder and harder and almost impossible.
Bailey is outraged when London makes fun of her clothing and hometown on her Internet show “Yay Me” and tries to talk some sense into her. But London ignores her, and only makes it worse for each thing she embarrasses. Meanwhile, Zack and Cody tutor the ship’s security guard when it turns out he didn't’t take his high-school equivalency test, but they start to argue over what is the best learning technique.
When the gang is banned from the Sky Deck, Zack and London are tired of always being bullied by Mr. Moseby, so they believe that he will get off their back if he got a girlfriend. When they later found out that Ms. Tutweiller is single as well, they trick them into thinking they are each other's perfect match using the webpage eHarmony. Meanwhile, Cody steals Bailey's dating questionnaire to try and impress her using her answers, but it turns out Bailey had put in almost only fake answers, which humiliates Cody.
All during a stop in India, London's original roommate, Padma, returns to the ship in need of London's help when her Mother is going to board the ship to visit her. However, it's not as easy as they think to cover up the fact that Padma hasn't actually been on the boat. Meanwhile, Zack and Cody climb up a mountain to reach spiritual enlightenment, but when they get to the top, the only things that get enlightened are their wallets.
The gang is thrilled when Maddie, the candy-counter girl from the Tipton Hotel, boards the ship, and everyone is looking forward to spending time with her. When Maddie becomes the target of a prince's love, she believes the days on the ship are going to be like Cinderella. However, when it turns out the prince is 8 years old, Maddie receives help from Zack, the boy with a crush on her and is never willing to let her go.
As the boat docks in Rome, the gang faces problems. Mr. Moseby attempts to eat at a fancy restaurant, but is disturbed by Zack and Cody, whom later get jobs in the restaurant. Meanwhile, London falls in love with a guitarist, but when Bailey finds out that the guitarist may only pretend to like her back, she must convince London that she is being scammed.
When a girl's father turns out to have ties to Harvard, Cody needs to find a way to impress him in order to reserve a spot. Zack turns out to have a crush on the girl already, and therefore, he convinces Cody into pretending to date the man's daughter in order for Cody to prove how reliable he is. However, trouble emerges when the girl's father spots Cody flirting with Bailey. Meanwhile, London and Bailey go to a hyptonist show that accidentally causes London to believe she is Bailey.
The twins are looking forward to the upcoming visit of their dad, but when their mother boards the ship unexpectedly, the perfect guy-weekend is ruined. Meanwhile, nobody knows that it's Mr. Moseby's birthday, but when London finds out, she decides to learn everything there is to know about Moseby to give him the perfect present.
When London can bring one friend with her on a trip to Outer Space, she must decide between Cody and Woody. Not being able to pick one, she hosts a bunch of competitions to find out which of them is the best spaceman. Meanwhile, Zack takes over the Senior Fun-Tertainment program on the boat, but he has to deal with a bitter old man not willing to do what he says.
When a girl is found floating in the ocean, everyone onboard the ship try to find out where the girl comes from while also helping her recover her memory. However, Woody becomes worried when suspicious evidence suggests she is a mermaid. Meanwhile, Cody watches how much garbage the passengers just throw away and is shocked.
When everyone gets a present from home, Bailey becomes homesick when her's reminds her of a festival she misses in her hometown. In order to make her feel better, Cody attempts to re-enact the festival onboard the ship, but London ruins everything by inviting Bailey's old boyfriend.
After injuring his leg, Mr. Moseby is required to relax to let the leg heal, but this turns out to be harder than expected when Moseby must face a whole lot of painful visits as well as being the person responsible for the Captain's upcoming party. Meanwhile, London's skills are put to the ultimate test when the Captain's gift smashes in the floor and she must re-build it.
Hannah Montana and the Russo family board the S.S. Tipton; Hannah for her concert in Hawaii and the Russo's for winning a competition. While the teens all get to know each other, we see London and Justin may be developing a relationship, Alex fakes her identity but can't remember her fake name, Cody tries to get tickets to the Hannah Montana concert for him and Bailey, and Alex pulls a prank that accidentally causes Zack to be framed.
When spotting a spy climb onto the ship and fighting a bad guy, the twins must protect a top-secret microchip as well as find another enemy among all the passengers. However, as they become more and more involved, it becomes more and more unclear if the spy really is the good guy, and Zack and Cody wind up captured by Red Finger.
London develops a crush on the ship's magician, but in order to get to his heart, she must first remove the one obstacle; his assistant. Meanwhile, when Zack constantly interrupts Cody and Bailey's dates, they find another friend for him to hang out with; Woody.
When Zack pulls a prank, Mr. Moseby and Ms. Tutweiller decide to put him in a position of authority, that should have a result of Zack becoming a model student. However, when this succeeds, all of Zack's friends start to dislike him. Meanwhile, Cody and Bailey have so tight schedules they barely have time for each other anymore.
The interest of making food suddenly becomes more interesting when Cody takes over the classes. However, his relationship with Bailey might end when all the girls start to flirt with him, making Bailey jealous. Meanwhile, London makes a fortune selling Zack's ruined artwork paintings, but all this is unknown to him as he just thinks London uses them to get a grade besides F.
When Bailey tells London her trick to succeeding in school, a perfume with smarticle particles, London gets addicted to it, and becomes a model student. However, when she overhears Bailey and Cody talking about the perfume as fake, she may get back to the low-intellectual mind she originally had.
As the boat docks in Thailand, London is shocked to uncover that her granny is a farmer and not a rich heiress as herself. Facing the physical challenges of actually working hard and not being able to do what she wants causes London to dislike her granny. Meanwhile, Cody attempts to make a video diary of how much he misses Bailey, whom is visiting London's granny, but is constantly interrupted by Zack.
After stealing Cody's paper, Zack winds up in an uncomfortable position where everyone somehow believes he has a phobia against bananas. Meanwhile, London goes crazy when her phone is confiscated, and Woody becomes addicted to Better Life.
Starting a new semester at Seven Seas High, the students get off to a bad start by by being lost at sea and stranded at a deserted island. With no way to be rescued, the students' skills are put to the ultimate survival test. But will it be enough to get back to the boat or will this be the end for the students?
A new member, Marcus Little, joins the gang as Zack's new roommate. But Marcus doesn't seem like any other teen boy, so the gang decides to find out what makes him so special. Meanwhile, Cody and Bailey fight against each other in various activities to find out which of them is the best at sports.
When Jordin Sparks boards the boat to perform a few of her songs, Zack and Cody, with the assistance of Marcus, attempt to write a love song for her. However, Cody believes his song is perfect until Marcus' opinion is spoken and the two of them get on each other's nerves. Meanwhile, London hosts a competition where the winner will get to spend a week onboard the boat with her, but the cute little girl who wins turns out to be evil and tries to steal London's identity.
As the boat crosses the Bermuda Triangle, Zack and Cody have a fight that results in them wishing they were only childs. When this happens they find themselves raised separately with no knowledge of each other. Zack is the nerdy one and Cody is the troublemaker.
When some attractive girls board the Tipton for a week, Zack and Woody create a fake beauty pageant to meet them, with the hook being the celebrity guest judge Marcus, and the catch being he didn’t know about their little plan, but agrees anyway. Meanwhile, London clears away Bailey’s shelf planning on winning and insults Bailey when she takes exception to London’s stealing of her space. This causes Bailey to enter with plans of beating London with Cody’s help.
The boat docks in Sweden, and the twins are shocked to learn that their ancestors were scoundrels and not heroes, according to Mayor Ragnar. Facing the emotional damage of the news, the twins seek information to find out if the story was real. Meanwhile, Mr. Moseby and Marcus visit a store to fix Moseby's broken nightstand, but it turns out to be a harder job than expected.
The gang is visited by an old friend, Esteban, who's getting married onboard the boat. However, Esteban's mother is unfortunately also on the cruise, and she does everything in her power to make sure Esteban and his future wife don't marry each other.
Cody makes up a web of lies that involves every one of his friends after he forgets to do his homework for the very first time, but it gets out of control. Meanwhile, Mr. Moseby and Zack get handcuffed together by the creepy ship counselor to see things from each other's perspective, but they are desperate to get the handcuffs off again.
Zack starts a fantasy football league after Mr. Moseby bans football being played onboard the ship. The game gets competitive after London joins and surprises them when she actually starts winning; with some luck and help from Kurt Warner. Meanwhile, after feeling depressed after getting laughed at, Cody gets Kirby to teach him how to play football.
After his visit to a Sherlock Holmes museum in London, Cody attempts to solve a mystery involving a stolen book. Meanwhile, Zack and Marcus are challenged to a game of croquet by London's British boyfriend.
The boat docks in South America and the Seven Seas High class visits an archeological site to help dig. However, Zack finds the crown of an ancient (evil) princess that takes over Bailey's body and captures Zack when he wants to keep the crown for himself.
A competition is set in place when Mr. Tipton offers one million dollars as the grand prize of a contest where everyone has to try and create the best new invention.
Zack, Cody and London fall asleep in history class, and each of them dream they are part of a classic fairy tale: London is the evil queen in "Snow White"; Zack is in "Jack and the Beanstalk"; and Cody is in "Hansel and Gretel."
A new assignment involves the students at Seven Seas High to simulate marriage.
The gang are assigned parts of a newscast. Zack and Bailey as the anchors, Woody as the camera man, London as the weather person and Cody as the field reporter. Cody uncovers a missing passenger plot in the midst
A robot Mosbey comes from the future to kill Zack because of something his decendant does in the future.
Bailey bets London 1 million dollars, or Bailey being London's slave for life. London finds it harder than she originally thought so she see's the ship's wacky Counselor for help. Meanwhile Moseby is doing the very same to get over his deathly fear of bees.
Due to numerous misunderstandings, Cody and Bailey break up while the ship is docked in Paris. Meanwhile Woody's bag gets mixed up with an art thief's bag, Moseby is excited to see the Tour de France and Marcus is investigating a Little Little impersonator.
Heartbroken over his and Bailey's breakup, Cody join's a non-religious monastery. Meanwhile, Bailey seeks break-up advice from Miss Tuttweiler.
Cody and Bailey argue over who gets custody of their lab rat Buck, so Kirby helps decide who gets it. Meanwhile Zack gets Woody to thinks he's becoming a mutant thanks to the rat's bite, so he can get it on with a cute girl.
Moseby and Emma schedule their own dances on the same night on the skydeck and compromise to hold both the Medieval dance and the Back to the 80's dance at the same time. Meanwhile Cody and Bailey rush to get dates for the night, taking advise from Zack and London.
A new waitress named Maya joins the ship, when Zack hits on her and fails he comes to realize he has fallen in love with her, so he takes some advice from Cody on how to win her over. Meanwhile, Dante who stole Marcus’s identity in Paris sneaks on board looking to work with him.
Cody competes in a Junior chess tournament against a worthy opponent from Russia. Meanwhile Zack, Maya, Woody and London become trapped under water in London's Shoe Submarine with no idea how to get out as everything is written in Russian.
Bailey returns to the ship, and construction on the new Aqua Lounge is held back when one of the portal cracks flooding the whole place. Moseby wants to know who did it, as Mr. Tipton will have the person responsible expelled. Meanwhile Marcus films a hip-hoperah he wrote himself.
Arwin visits and programs the ship with a female super computer that falls in love with Cody. Meanwhile Zack tutors Woody and London in fitness so they can pass PE.
While preparing for a video game tournament, Zack is becoming whipped in his relationship with Mia. Meanwhile Bailey and London participate in community service, taking care of the passenger's children.
Zack and Cody visit their mom on the set of a Japanese soda commercial, but when Zack trashes it all 3 are forced to become taste testers. Meanwhile Woody beats a Sumo wrestler in a match, who gets so upset he moves in with Woody. All the while London is hiding from Moseby so she doesn't have to go to the dentist.
While the ship is docked in Louisiana at the sight of a shipwreck, Zack is haunted by the former captain who is blamed for it's disaster. Zack gets Cody and Woody to help find the truth about what really happened to clear the captain's name. Meanwhile London and Bailey help Moseby get over his fear of playing the piano in public.
It's Senior Ditch Day, and while Zack, London and Woody try to get in a very exclusive club, Cody and Bailey go to class because they don't want to ruin their perfect attendance. All Miss Tutweiller wants to do is finish her romance novel rather than teach 2 overachieving students, so she gives them an assignment to 'have fun.'
Woody asks Cody to hang out with his sister while he completes an over due assignment. Everyone is surprised at how beautiful she is. Meanwhile London tries to find her twin.
After London refuses to donate anything to charity, she has a dream where her talking mirror (from the original series) takes her to the past, present and future. The past shows that she used to be a really sweet girl, the present shows what everyone is doing on Christmas eve and the future shows London what her future will end up as. Meanwhile, Zack keeps being late for his shifts at the drink counter, so Moseby tells him to be there at 6am on Christmas day.
London helps Bailey get back to Kettlecorn for her grandma's 92nd birth day, while on the ship Moseby tricks Zack and Woody into playing basket ball against his little brother who just so happens to be an NBA all-star player
Cody rushes to Kettlecorn worried about Bailey who was stranded in the previous episode, tries to compete against Moose for Bailey's affection. Meanwhile on the ship, Zack rents out all the student dorms for a family reunion so he has money to take Maya out for their 3rd month aniversary.
London is missing since the tornado, and Bailey's home is destroyed from the storm, so Cody tries to figure out a solution to both problems.