The movie opens with Apocalypse Inc. setting up a fake news report, claiming that there is a contaminated area in Japan that needs cleaning up. The Toxic Avenger, who has become a celebrity hero in Tromaville, sees this report and decides to travel to Japan to help.
Once in Tokyo, the Toxic Avenger meets up with his new sidekick, a Japanese girl named Masami. Together, they take on a variety of evil villains, including a mad scientist known as the Doctor, who uses mutant creatures to do his bidding.
Meanwhile, back in Tromaville, Apocalypse Inc. is taking over the city. They install a new mayor to do their bidding, and begin building a new factory that will pollute the town's air and water. Only the mayor's assistant, Claire, seems to realize that something is wrong.
As the Toxic Avenger fights crime in Tokyo, he begins to uncover the truth about Apocalypse Inc.'s evil plans. He and Masami team up with a group of Japanese rebels to take down the villains and save the city.
Eventually, the Toxic Avenger returns to Tromaville and confronts Apocalypse Inc. in a final showdown. With the help of his friends and allies, he is able to defeat the corporation and restore order to the town.