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.

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

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.

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.

The SS Tipton is going straight in the path of endangered blue whales motivating Zack, Cody, Bailey, and Marcus to try their best to change the ship's course. They lock themselves into the engine room hoping the whales will safely pass, however they discover it's not as easy as it seems. Cody begins to faint due to heat exhaustion, Marcus becomes desperate for water, and Zack loses it and tries to break free. Eventually, Kirby and Mr. Moseby break into the engine room to attempt to stop them, but after seeing the whales on Cody's laptop, they decide to go along with plan.

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.

Bailey bets London $1 million dollars that she cannot go on one week without insulting her, so London asks Mr. Blanket for help to try not to insult Bailey. When Bailey loses the bet, London insults her one million times. Meanwhile, Cody attempts to avoid the assaults of a seagull after not permitting the seagull to eat fries.

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.

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.

Jordin Sparks comes aboard the S.S. Tipton and Zack, Cody and Marcus try to write a song for her. Meanwhile, as one of London's Yay Me! contest, one of her fans gets to spend a couple days with her on the ship, but London's fan is a little crazy.

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.

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.

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

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

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.

A microchip with secret information on it goes missing and the twins help a spy recover it. Cody gives the chip to Bailey, telling her to hide it and not to look at what's in it, but Bailey looks it up on her computer anyway. When Cody finds out that Bailey ignored him, breaking her promise, he has mixed emotions. Bailey kisses Cody on the lips as a way of telling him he can trust her, so he forgives her.

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.

Zack and Cody talk to Mayor Ragnar when the boat docks in Sweden, and they are shocked to learn that their ancestors were scoundrels and not heroes like the twins originally thought. Meanwhile, Moseby gets help from Marcus to find the missing screw for his nightstand, but they accidentally get stuck in a furniture store.

When London's father gives her one million dollars to find an invention to market, she enlists her friends to come up with a unique invention and offers them the cash as a prize. At first everyone comes up with their own ideas, but then they combine their resources, wreaking havoc on the ship with their multifunctional robot.

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.