Zack, Cody, Mr. Moseby and London set sail on the S.S. Tipton for their semester at sea - where they get acquainted with their new home and roommates, including Bailey, the new girl who pretends to be a boy in order to secure a spot on the prestigious cruise liner.
London is unhappy that her father is making her stay on the S.S. Tipton for school, so she flees to Parrot Island. When the ship makes a special trip to pick her up, Zack and Cody end up in jail, and Bailey has to use her pig, Porkers, to rescue them.
Zack uses up both his and Cody's meal cards buying things for all of the girls on the ship. Zack thinks that Cody can win a yo-yo contest, that has a grand prize of $1,000. Meanwhile, Bailey is mad that London is hogging all the space in their cabin, so she fakes a "Sea Snark" attack.
Zack has a crush on Violet, but must deal with her wealthy boyfriend Ashton and snooty mother who will do anything to keep Zack and Violet apart. Meanwhile, Cody referees an intelligence test between London's dog Ivana and Bailey's pet pig Porkers. When Zach is framed for stealing the "Kidney of the Sea" necklace, it's up to London's dog, Ivana, to prove his innocence.
London and Bailey try 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 showgirls show on the ship.
Cody tries to impress Bailey at their school dance and fails. He then is miraculously able to go back in time to try and fix his mistake.
The S.S. Tipton visits Greece. Bailey flirts with the tour guide, which makes Cody jealous. To impress her, Cody accidentally gives Bailey an ancient amulet as a gift. Meanwhile, a dream about Greek history, inspires London and helps her write a speech for her father.
The class has a school project to complete and Cody chooses Bailey to be his partner. Cody tries to catch a famous sea monster but keeps failing and dissapointing Bailey. Upset that Cody chose Bailey, Zack tries to sabotage his project.