The film begins with a trip to the beach for Tom and Jerry who soon get into a chase. On the same day, the duo later encounter Jonny Quest and Hadji, along with their canine companion Bandit. Tom fights off an evil cat army and sends them to retreat. Later, they meet Race Bannon who takes them to Quest Labs where they meet Jonny's father, Dr. Benton Quest, who happens to have the Q sphere, a device that will solve the world's energy problems.
Meanwhile, Dr. Quest's nemesis, Dr. Zin soon finds out about the device and he sends his bumbling henchcats Tin, Pan and Alley to steal the device and kidnap Dr. Quest. That evening, Tom, Jerry, Bandit, Hadji, Dr. Quest, Jonny, and Race are having dinner. Tom is dissatisfied upon only having a bowl of milk. He tries to get the steak from Bandit which that dog isn't happy about, leaves himself still hungry when he and everyone else go to bed for the night. Before heading for bed, he learns and memorizes the security code, which is 1-2-3-4.
The security system is unlocked as Tom helps himself to the food and as a result, the cats easily break into the Quest Labs and abduct Dr. Quest along with Race and steal the device. Jonny Quest and Hadji wake up to see what has happened, rushing to the scene. They pinpoint to the location where the cat army has taken Dr. Quest and Race and rush off to rescue them. They head to Zin's island where Jonny and Hadji are captured by Zin's robots due to Tom's antics, However, Tom and Jerry escape.
Jerry decides to help them and Tom, who resist to help them, joins the fight where they help Dr. Quest, Jonny and Hadji escape and successfully destroy the volcano which was to attack the White House. Zin tries to escape on his escape pod, but it is stolen by his henchcats, who get tired of his abuse, forcing Zin to hold on to the pod. Tom, Jerry, Jonny, Hadji, Dr. Quest and Race escape from the island and are awarded by the President and the film ends with Tom chasing Jerry after he made fun of Jerry's small medal.
