After making plans to spend spring break with his girlfriend Bailey Pickett (Debby Ryan), Cody Martin (Cole Sprouse) decides to leave the SS Tipton, a large cruise ship where he attends school, to work as an intern for...展开Dr. Donald Spaulding (John Ducey) at a prestigious research firm instead. He does so in hopes of obtaining a scholarship to Yale. When Cody's twin brother Zack (Dylan Sprouse) reveals Cody's plans to Bailey before Cody could, however, she becomes infuriated that Cody canceled his plans with her and refuses to speak to him. Meanwhile, Zack asks Cody for his car, which their parents will give to Cody when he goes to college, but Cody refuses. However, after Zack runs a billion-dollar submarine into the seawall in an attempt to impress a cute science assistant, and Cody does the same trying to stop him, the equipment is lost and Cody is kicked out of the program and fired. Furious, Cody tells Zack he hates him and vows to never forgive him, claiming they may be twins, but they definitely are not brothers. Elsewhere, the hotel heiress London Tipton (Brenda Song) accidentally eats a fruit given to the dolphins which allows her to comprehend them.
The Martin twins later learn that although Cody will no longer be eligible to work as Dr. Spaulding's intern, both boys are ideal for the Gemini Project, a massive project by Dr. Ronald Olsen (Matthew Glave), who studies the physical and emotional connection of twins. Though it takes them much thought, the brothers agree and land themselves in a camp among hundreds of other twins. Dr. Olsen explains to them that the purpose of the project is to create an emotional bond between people that he hopes will put an end to evil in the world. By doing this, according to Dr. Olsen, he must form a bond between twins. Over the course of the project, which uses the same fruit as Dr. Spaulding's experiments, Zack and Cody form a bond: first a physical bond, in which they can sense what the other is feeling, then empathy, or an emotional bond. After they develop these bonds, they overhear a conversation that reveals that Dr. Olsen has evil intentions. Meanwhile, Bailey discovers Cody's letter and reads it. She realizes Cody only wanted to obtain a scholarship to Yale and goes with London and Woody to find him.
At the institute, London learns from a dolphin that Zack and Cody are at the Gemini Project and alerts Dr. Spaulding who claims that the Martin twins may be in danger. Bailey calls the manager of the SS Tipton, Mr. Moseby (Phill Lewis), to the site of the Gemini Project while they all go to save Zack and Cody. During this time, the brothers attempt to flee the island and the twins, who are now mind-controlled. However, they are captured and taken back to the laboratory, where Bailey, London, Woody, and Dr. Spaulding find them. Dr. Olsen reveals that he is Dr. Spaulding's evil twin and explains that he spied on Zack and Cody earlier in the movie. After telling each other off, Zack and Cody begin to merge, but the merge is unsuccessful because the twins get into an argument that escalates into a physical altercation, ultimately destroying the Gemini Project. Ronald claims he will merge everyone and attempts to reboot the machine, but he is stopped by Cody who quickly forms a plan, and he and Zack give the special fruit to the Spaulding twins, who finally understand each other by telepathically discovering that they wanted to be like each other all along. Mr. Moseby comes in with the police who arrests Ronald. Zack and Cody now understand that they make a "pretty good team."
Afterward, Cody and Bailey have reconciled and visited landmarks together and Zack is driving his car, which Cody finally agreed to let him have. On the dock, Zack parks the car in a shipping area and sees his friends and brother on the SS Tipton. Unfortunately, the car is crushed by a shipping crate containing London's summer clothes. While Zack lets out a cry, the movie ends with Mr. Moseby saying, "Well, spring break is over. Now if I could just make it to summer vacation."