The film begins in a big ocean, which is having a huge storm with loud thunder. A big ship is sailing on that ocean. On the ship, a group of pirates are holding the mainsail. All of the pirates are afraid of the thunderstorm. After that, it continues with Tom the cat and Jerry the mouse sleeping in the cabin of the ship. Ron uses a slingshot to get them on deck, sailing to find the Lost Treasure of the Spanish Mane. A wave crashes against Ron's ship and along with it, a bottle containing the map Ron was looking for. Tom keeps the map hidden for himself, but the skull, which happens to be the ghost of the Spanish Mane's captain Don Diego de Clippershears, warns Tom that the map has to be returned to the ocean by sunset tonight or the curse begins. Tom and Jerry also have a run-in with a giant squid. However, Tom manages to escape by pushing a cannon onto it.
At that point, Ron's ship is attacked by a blue pirate ship captained by Ron's brother Blue Pirate Bob. Ron and Bob hardly speak, but are translated by their parrot companions, Stan (red parrot) and Betty (blue parrot). A battle ensues between rival pirate crews and including Spike, Bob's mascot. After Ron retrieves the map, he begins firing on Bob's ship. Ron and his pirate crew celebrate as Ron checks the map. Jerry decides to eye the map and make a copy of it on his bandana. Suddenly, the skull appears beginning the curse. Ron is upset with Tom for not telling him about the curse (Tom had intended to tell him about it, but was unable to do so, due to the fact that he is a mute character). The ghost manifests into a skeleton crew of pirates and takes over the ship causing Ron's crew to abandon ship. The lifeboat manages to land on top of the same giant squid Tom ran into earlier. Angered, Ron puts Tom to work by making him row all the way to Yo-Ho Island where the Treasure of the Spanish Mane is buried. However, Tom decides to leave Ron's men stranded and uses an oar to reach Yo-Ho Island. However, a shark finds Tom and Jerry and they have trouble along the jungle of Yo-Ho Island! Jerry gets on a butterfly while being chased by Tom over the quicksand pit. But Tom gets trapped in the quicksand, so Jerry had to save him. After pulling Tom out, they had to find somewhere to be safe from the pirates.
Upon reaching the island, Tom and Jerry run into Barnacle Paul (also known as Purple Pirate Paul) and his non-talkative purple parrot Chuck. Paul has a crew of monkeys on the island and tells Tom and Jerry about how he and his brothers Ron and Bob made maps for a living and accidentally discovered the map of the Treasure of the Spanish Mane. Paul has seen enough of the map to know the island, but not enough to know where to look and is discouraged searching for it for over 40 years. Tom and Jerry go on their way when Ron shows up and tells Paul that Tom had the map. Tom and Jerry manage to dodge the pirates and monkeys to reach a volcano where they finally find the entrance to the tomb of Don Diego de Clippershears.
Don Diego decides to test Tom and Jerry by activating his security system to keep thieves out of the tomb: a stone guardian resembling a chicken, the mascot of the Spanish Mane. Tom and Jerry manage to defeat the guardian and unlock the gate. Tom decides to leave Jerry behind and head inside (due to his greedy nature and partially resentful of Jerry when the latter uses him as live bait to defeat the guardian), but doesn't listen to Don Diego tell him about a booby-trapped stairwell. Jerry decides to use his head by using Don Diego as a shield. At the bottom of the stairwell, Tom revives and head into a next room filled with runes. Jerry has to find a rune that resembled one Don Diego shown for a brief time. If Jerry picked a wrong rune, a lightning rod would electrocute him. Jerry picks the wrong rune, but the lightning rod zaps Tom who is about to pounce on Jerry.
Jerry reaches the cave where the Treasure of the Spanish Mane was in plain sight. Jerry knows that a treasure this large would have to be guarded. Tom rushes in anyway but is shocked to see the same giant squid as the ultimate guardian. However, the squid recognizes Tom and shrieks in fear, causing a rock to crush it, much to Don Diego's chagrin (who, upset with the failures of his magic traps, loses his will for make victims to his treasure). After retrieving the treasure, Tom decides that he doesn't need Jerry and tosses him away. However, Ron is standing beside him furiously with Tom and accuses him of planning to steal the treasure for himself. Ron and Paul then begin to fight for the treasure as Bob comes sailing in with his ship fully repaired. Angry with their parrot counterparts, the three brothers shoo the parrots away and continue fighting. Before getting into the fight Paul watches the fight between Bob and Ron and takes off his hat, lamenting how it's just like old times. Jerry, seizing the opportunity, manages to sneak the treasure away by way of dolphin. Tom goes to pursue in a lifeboat, but every lifeboat onshore is sabotaged. Spike notices that Bob's ship is sailing away and the pirates realize they're now stranded. Tom makes a last-ditch effort to get on board the ship using a catapult from a palm tree. Spike grabs Tom and both are catapulted onto the ship. Jerry offers a golden bone to Spike as a token of friendship and decides to deal with Tom.
In the ship, Jerry and Spike control the ship while Tom swabs the deck. Meanwhile, Ron, Bob and Paul and the rest of their men remain on the island, running from the stone chicken. As Jerry Mouse, Tom and Spike sail away happily ever after, Stan, Betty, and Chuck finally find a leader they can relate to.
- The movie makes extensive use of the classic MGM Tom and Jerry sound effects, including the famous Tom scream. Also, Mark Watters' music comes closer to original Tom and Jerry composer Scott Bradley's jazzy scores from the 1940s and 1950s than many of the other direct-to-video films.
- The Skull's laugh are rather similar to Mark Hamill's trademark Joker laugh.
- Dee Bradley Baker - Jerry
- Charlie Schlatter - Tom
- Kevin Michael Richardson - Red Pirate Ron, Blue Pirate Bob, Purple Parrot Chuck
- Kathy Najimy - Blue Parrot Betty
- Charles Nelson Reilly - Red Parrot Stan
- Wallace Shawn - Barnacle Paul
- Mark Hamill - The Skull
- Main article: Tom and Jerry: Shiver Me Whiskers/Gallery