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

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.

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.

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

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 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.

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.

Cody tries to find out who stole a valuable book.

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.

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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, 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.

Esteban boards the boat to get married, however his mother doesn't approve of his future wife.

While searching through an archaeological site in South America, Zack awakens the spirit of an ancient princess.

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.

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.

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.

London visits her grandmother in Thailand. Meanwhile, Zack asks Cody to go on a double date with him.

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.