The movie begins with the Planet Express crew attempting to repair the tear in space-time caused by Bender in the previous movie. However, the crew discovers that the tear doesn't lead to an alternate universe, but instead opens up a portal to another dimension.
After the portal is opened, a tentacled creature named Yivo emerges from the other side and quickly befriends the inhabitants of Earth, including Fry, who falls in love with Yivo. However, not everyone is happy with Yivo's arrival, and a group of protesters known as the "Legion of Mad Fellows" begin to voice their opposition.
Meanwhile, the Planet Express crew begins to notice strange things happening around them, such as objects disappearing and mysterious messages appearing. After investigating, they discover that Yivo is actually a massive hive-mind entity that has attached itself to Earth and plans to assimilate all life on the planet.
As Yivo's true intentions are revealed, Fry must choose between his love for Yivo and his loyalty to his friends and fellow humans. In the end, the crew devises a plan to defeat Yivo, but not before they are sucked into its tentacled portal and sent into a black hole.
The movie ends with the Planet Express ship reappearing in an alternate universe where they encounter a new set of adventures and challenges.