The film begins off with a Star Wars-styled title crawl. After the credits, the film cuts to the USS Consolationprize (EEK-U812) being attacked by a spacecraft resembling a Star Destroyer. We are then introduced to the ship's crew, Captain Kwirk and Mr. Spuck. A menacing figure named Dark Vapor then appears telling them that they are to be captured as part of the Rebellious Alliance. Upon realizing that the rest of the crew won't appear due to budget cuts, they escape in a shuttlecraft, and land on Earth, in the year 2001. They climb over a ridge to find a monolith, which belongs to a cigar-smoking Star Child. He says his monolith is broken and the universe is falling apart because of it. He states it's up to Kwirk and Spuck to repair it. They are also told that the dark smell of the force wants to steal the monolith for its power. But both sides can summon any warrior from any universe (with Mr. Spuck's "tape recorder") to help their side of the fight.
The film tells the story of two good friends and housemates, Andrew, an agoraphobic travel agent, and Dave, a loser who works in an office. Dave is fired from his job after his girlfriend frames him for embezzlement, Andrew is falsely accused of attempted child molestation, and their house is to be demolished by day's end. Both of them hide inside the house as police, city officials, and outraged neighbors surround it. Dave and Andrew open their front door and discover that the entire world beyond their house is gone, replaced with a featureless white void.
Nuvo hangs out with a group of pals who have an inordinate interest in getting high, and like his buddies he's always interested in the next new chemical to come along. Nuvo and his friends Swatch, Chad, Theo and Ping. have heard about a new drug called the Helix, but while they'd like to give it a try, word on the street is that it has rather unpredictable effects—used properly, it can give its users deep enlightenment, but a bad trip can literally cause you to lose your mind. Nuvo's interest in the Helix is more philosophical than recreational, and he falls in with two mysterious figures, Infiniti and Orpheum, who are searching for The Other One—a person who can break through to a new level of understanding while tripping on the Helix.
Bruce Campbell plays William Cole, the wealthy CEO of a U.S. drug company who travels to Bulgaria with his wife, Jackie (Antoinette Byron) in the hopes of diversifying his company's financial interests. Cole is a stereotypical ugly American who constantly complains about the lack of Americanization of the former communist country. They're driven to a hotel by a taxi driver, and former KGB agent, named Yegor Stragov (Vladimir Kolev), in which Yegor gives William a ring to give to Jackie. While William is at the construction of a subway, Jackie secretly cheats on William with Yegor.
The newly established P-Fleet travels to a remote region of space. They approach an anomaly, identified as a "maggot hole". On the bridge of the C.P.P. Potkustartti, Captain James B. Pirk (Samuli Torssonen) reminisces about his experiences since the end of the previous film, Star Wreck V: Lost Contact. Pirk was stranded on Earth at the end of the 20th century, his spaceship destroyed, his crew dispersed to avoid changing Earth's history.
Tom is chasing Jerry around using established plot and action devices until they arrive at the "Space Place". The staff there is testing dehydrated food. It is announced that Buzz Blister (voiced by Jess Harnell) and Biff Buzzard (voiced by Billy West) are going to Mars. In the process, Jerry and Tom are caught during the speech (first misunderstood as aliens due to Tom getting hit by green paint backstage), and they try to capture them, but only Tom is caught and thrown out. During the dehydrated food testing, Jerry knocks over a cup in the process, and all the food comes to life, and as a result, the food goes all over the place in an explosion. Soon the staff tries to catch Jerry, but figure only Tom can catch him, so they bring him back to the base and give him a mission to "eliminate" Jerry, and at the end of the chase, they are chased into a rocket ending up at Mars. They discover a giant black wall, similar to the black monolith in the Space Odyssey series. A green female alien named Peep (voiced by Kathryn Fiore) arrives with an alien dog, Ubu and two more Martians arrive. Jerry is mistaken for the “Great Gloop”. After much calamity and a discovery that Jerry is not the Gloop, Tom, Jerry and Peep (since she knows this was all a misunderstanding and trusted Jerry from the very beginning) steal a flying saucer, so they can get back to Earth and warn everyone about a potential attack by the Martians. They manage to stop them, but the “Invince-a-tron” eventually arrives on Earth and begins to suck everyone up with its vacuum. Tom, Jerry, and Peep stop Invince-a-tron, using a bone to get Spike into his brain and make it malfunction, much to Spike's nervous breakdown in the end. At the end they are thanked and awarded with a Hummer by Arnold Schwarzenegger (uncredited) as the U.S. president. Before they could even drive it, they are attacked by the Invince-a-tron again but this time controlled by Spike (mad for the destruction of his precious bone) who chases after them. Peep comes with the ship and rescues Jerry, but leaves Tom behind (for no apparent reason). Peep kisses Jerry with him being blushed as the iris closes in. At the ending scene, Biff and Buzz are seen cleaning the mess as punishment for lying that there is no life on Mars, soon they start to argue about it and fight as Tom is being chased by the Spike controlled Invince-a-tron in the background.
Sometime in the future, mankind has depleted all energy and fuel sources, however they have somehow engineered a way to use human excrement as fuel. To reward production, the government hands out extremely addictive, popsicle-like "Juicybars", which in turn also makes them constipated. Aachi and Ssipak are street hoodlums who struggle to survive by trading black market Juicybars. Through a chain of events involving their porn-director acquaintance Jimmy the Freak, they meet a porn star named Beautiful, whose defecations are rewarded by exceptional quantities of Juicybars. For that reason, Beautiful is also wanted by the violent blue mutants known as the Diaper Gang (led by the Diaper King), the police (most notably the cyborg police officer Geko), and others.
When inventor Mariko Tanaka (Hiroko Yakushimaru), who works for Hitachi appliances, accidentally re-engineers a washing machine for time travel, the Japanese government then convinces her to go back in time to prevent the passage of a fictitious law that would prevent the usage of real estate as collateral for loans, which was a major cause of the bursting of the Japanese asset price bubble. However, when contact is lost after she goes back in time, the government then sends Isao Shimokawaji (Hiroshi Abe), who works for the Finance Ministry's Emergency Response Bureau to convince Mariko's estranged daughter Mayumi (Ryoko Hirosue), to go back in time to investigate (other ministry officials tried to use the time machine but all they ended up with were faded socks).
A month after the universe was ripped open in Futurama: Bender's Big Score, people decide to go on with their lives. Amy and Kif get married. Fry starts dating a girl named Colleen, but breaks up with her when he discovers she has many more boyfriends.
The Planet Express crew visits Amy's parents, Leo and Inez, who are destroying the "old" Mars Vegas and constructing a more extravagant one. A group of eco-feminists (calling themselves "eco-feministas") led by Frida Waterfall protest the destruction of the environment, leading to an accident wherein a piece of Frida's jewelry lodges inside Fry's brain. The destruction upsets Leela, but Leo has bribed Professor Farnsworth to rubber stamp the project as environmentally friendly. Leela saves a Martian muck leech, the last of its species, from the site.
The film starts out with an assassination attempt on a political candidate by a Geisha (that turns out to be a robot) and two scantily-clad women wearing Tengu/Goblin masks. The goblin-clad women violently (and phalically) take out the body guards (notably shooting shuriken out their butts) as the politician is menaced and wounded by the robot geisha who has a circular saw blade in her mouth. Suddenly, another person named Yoshie (Aya Kiguchi) appears, reveals herself as a robogeisha, and destroys the villainous robot.
A band of ninja warriors, led by an Iga Ninja named Yamata and his comrades Jinnai and Nezumi, are assigned to investigate the crash of a mysterious object from the sky. Upon arriving at the crash site, they discover the remains of other ninjas that have been brutally torn apart. Shortly after joining forces with another band of ninjas led by the kunoichi Rin, they encounter a boy whose village was massacred by an unknown assailant. Before they can get any further explanation from him, the ninjas are attacked by the assailants, who reveal themselves to be aliens from another planet. After a grueling battle that takes the lives of several ninjas, Yamata, Rin and Jinnai kill three of the aliens, but one of them retreats and takes Jinnai with it. A cowering Nezumi rushes back to his home village, only to see the villagers massacred by the aliens. He runs for his life, but is cornered by the alien, which swiftly decapitates him as his head lands on a temple post for a crow to feed on.
At Kinetech Labs, an inventor named Allan Topher designs a robot for search and rescue, but when he finds out that the robot will be used for military purposes, he programs the robot to flee. The robot escapes but is damaged in the process. It is discovered by 12-year-old Henry Keller, who fixes it and names it Cody. The robot does not remember its past, and Henry and Cody develop a friendship. Eventually, Cody regains his memory and Henry gives Cody back. The inventor feels guilty for taking Cody away, so he returns the robot to Henry. Allan meets Henry's mother, Joanna, and they get along really well. Kinetech finds and corners Cody and Henry. Cody activates another function of his, and takes off with Henry, flying high up into the sky. They reunite with Meagan but when they call their mother, they find out that Kinetech has kidnapped both their mother and Allan so that they can get the robot back. Meagan, Henry and Cody embark to save them and to bring down Kinetech.
Zenon Kar (who is now 15) is two years older in the year 2051 but none the wiser about the dangers of meddling, but when she shows Nebula a new game and how to play it she inadvertently empties out Commander Planks Office and is assigned work detail in the Alien Patrol lab. Worse the space station is now under command of the military and General Hammond is assigned to command the station. Commander Plank, very furious ,comes out of his office and stops Zenon. Even worse, he assigns Zenon to look after his daughter who turns out to be her old nemesis, Margie, who's demanding and threatens to have her dad kick Zenon and her family off the space station if Zenon doesn't obey her.