Computer whiz kid Will Farmer's (Matt Lanter) neighbor Massude comes to Will having a problem with his computer. Will takes the computer and hooks his own up to it and discovers that Massude's brother is using his online banking to make huge profits. Since he needs $550 to go on a chess trip, Will steals $500 from Massude's account to gamble on an online gaming site that uses games that are based on terrorist attacks. Will later discovers that his best friend Dennis changes it to $5000. He ends up winning $25,000, with the aid of his mother, who knows about biological agents. Little does he know that the online game he plays is actually part of a sophisticated piece of U.S. government spyware designed to find potential terrorists based on how well they perform and bet on the games. The spyware program is run by a new, advanced artificial intelligence system called R.I.P.L.E.Y. (an acronym that is not explained in the film, nor by its makers), which has ultimate control over every American electronic system in order to combat terrorism.
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.
In the near future, Ueno is a man who has been raised with his parents' cyborg maid Maria. His parents pass away while he is a teenager, leaving Maria to care for Ueno. As an adult, Ueno's attachment to Maria leads him to attempt to program her for sex. This attempted consummation of their relationship fails, and when Ueno is an old man, Maria's power supply comes to an end, leaving Ueno alone. Meanwhile, a series of rapes occur in the city and Detective Yuri Akagi suspects a droid is responsible.
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.
The film takes place at an undetermined point in the future, when humanity has developed advanced robotic technology with enhanced artificial intelligence. This includes the use of cybernetic organisms (or cyborgs) called the TR-4 (all TR-4s are played by Paul Logan) for general labor. After being reprogrammed by the newest model TR-5, the machines instigate a cybernetic revolt against humanity, bombing cities and sending thousands of armed, identical TR-4 androids to eradicate all human life.
Taking place three hundred years prior to the events of the first film, the narrator describes how the government knew what was happening. A woman is seen driving recklessly in California while arguing over her cell phone. Police officer Ryan Hadley (Bruce Boxleitner) pulls her over and gives her a warning. The man calls her back, but she tells him off and throws the phone down; the phone then transmorphs into a robotic spider and kills her.
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.
Donald visits the "Museum of Modern Marvels" which showcases various futuristic electronic appliances and inventions. He uses a quarter on a line to get in (this allows him to keep his money and get in as well). Once inside, he is confronted with the "Robot Butler", a robot who takes hats ("Your hat, sir.") After Donald's hat is taken away from him, Donald uses a magic trick to produce another hat (similar to the way he produces flutes in The Band Concert). He says, "So!" and continues on his way. He first encounters a robotic hitch-hiker, which activates when he makes driving noises. However, when he laughs at it, it punches him in the face. Next he goes to the wrapping machine, which says "Do not touch" but Donald ignores the sign and hops on. When he pulls a lever, the machine proceeds to grab him in two robotic arms, put transparent wrapping paper around him, and put him in ribbons, like a package. He manages to break out by vigorously shaking, and continues exploring.
Project Questor is the brainchild of the genius Dr. Emil Vaslovik, a Nobel laureate. Vaslovik had developed plans to build a super-human android. A team of the world's foremost experts is able to build the android, even though they do not understand the components with which they are working — they are only able to follow the instructions, and install the parts, left by Vaslovik, who has disappeared. Attempts to decode the programming tape were worse than merely unsuccessful—they also erased approximately half of the tape's contents. They decide to substitute their own programming, over the objections of Jerome "Jerry" Robinson (Mike Farrell), the only team member who had actually worked with Dr. Vaslovik. He is overruled by the head of the project, Geoffrey Darrow (John Vernon). When the android's body has been finished, the new tape is loaded, but with no apparent results. In desperation, Robinson persuades Darrow to allow Vaslovik's tape — what remains of it — to be loaded. Again, the team is disappointed, as there appears to be no response.
A few survivors have dedicated themselves to preserving and protecting what is left of mankind; among these is former Army Captain John Thomas Garth (Grant Show). Approached by Lapierre (Steve Bacic), a former comrade now employed by eco-profiteer Anton Reich (Art Hindle), Garth is made an offer he cannot refuse. In exchange for his father's and other's survival, Reich agrees to lead a small team of mercenaries into the impenetrable Vincent estate to "liberate" the priceless works of art that had been stored there. Accompanied by reconnaissance specialist Fernandez (Naomi Gaskin), sniper King (Matthew G. Taylor), and tech genius Ebershaw (Wayne Ward), Garth must find a way to circumvent Encrypt, the deadly computerized security system surrounding the estate. Other obstacles include the Rook, a killer robot, and Diana (Vivian Wu), the holographic security chief of the estate. With the help of Lapierre, Garth destroys the Rook and discovers that it actually protects a device that can restore the ozone layer. With the help of Diana, Garth triggers it, but presumably dies soon afterwards.
The film begins by depicting the development process that eventually results in the creation of the main character. It is explained that in a robotics laboratory, five androids were created as part of an experiment, each one identified with a different color, but one turned out to be different. The yellow one developed the ability to think and learn, to the point that it escaped the facility in which it had been created and became a part of society for 18 months. Rather than seeing humans as enemies or a threat to its own survival, it was "making decisions, and observing us and learning." A SWAT team is sent after Yellow, chasing him through several countries and finally tracking him down in Shanghai. The film concludes during the encounter between the android and the SWAT team, with a voice over suggesting the birth of a new era, with AI becoming part of our society.
Following the mysterious disappearance of an oil rig and a reconnaissance mini-submarine in the Gulf of Mexico, scientist Dr. Margaret Adams (Nicole Dickson) initiates the Armada Program, which consists of giant robots designed for deep sea rescue. The three robots—piloted by Red (David Chokachi), Tracy (Jackie Moore) and Jim (Treach)—dive nearly 800 fathoms to the sea bed, where they not only discover the mangled remains of the oil rig, but encounter the monster that brought it down. Red pursues the monster against orders from Admiral Hadley (Graham Greene), prompting the Admiral to order every naval fleet on the East Coast to converge to the oil rig's site. Red emerges on a beach to warn the bystanders to leave the premises for their safety when he is suddenly attacked from behind by the monster as their fight takes its toll on the city. An F-18 Hornet piloted by Spitfire (Jared Cohn) assists Red in taking the monster down. Red, however, is arrested for disobeying a direct order. He is locked in solitary confinement until he is briefly released by Adm. Hadley and later given a medal of honor for his heroic actions before serving the rest of his confinement.
Not long after Megatron's demise and the restoration of Cybertron, the Autobots celebrate as Bumblebee is promoted to warrior class by Optimus Prime. The festivities end, however, when Optimus sets out on a journey to find the AllSpark, the source of new life on Cybertron, and takes Wheeljack with him to find it so that new Transformers can come into being. Ultra Magnus is left in charge in Prime's absence to hunt down the missing Starscream, Shockwave, and Predaking with the other Autobots. Meanwhile on Earth, at the bottom of the ocean, Megatron's consciousness is reawakened by Unicron, who seeks to destroy his arch-enemy Primus, the very core of Cybertron, and requires Megatron's body to do so. Unicron reformats Megatron into a body with new upgrades before heading to Cybertron. In the meantime, Ultra Magnus and Smokescreen continue to search for the fugitive Decepticons in the Sea of Rust, but are soon attacked by the Predacons Skylynx and Darksteel. After a brutal fight, Magnus is severely damaged and Smokescreen barely makes it through the space bridge with him. The damage is so critical that the Autobots are forced to call in Ratchet from Earth for assistance while the Autobots deduce that the two new Predacons must be creations of Shockwave. Meanwhile, Starscream and Shockwave are revealed to have restarted "Project: Predacon" and plan to create an army with Skylynx and Darksteel being their first creations.
In the year 2045, a Los Angeles Police Department detective and his new partner - a state of the art crimefighting robot cop - are tasked with recovering a runaway Telepresence android containing the consciousness of the Mayor's daughter, who remains unaware that she is a human mind in a machine body. Their investigation takes the unlikely partners into the heart of the Zone - a vast, irradiated section of California created by earthquakes years earlier - where they recover the Mayor's daughter but are betrayed by corrupt fellow officers, forcing the trio to fight their way out of the Zone through mutant ghettos, gang territories, and even the LAPD itself.
Mr. Hublot is a man who lives in a tiny apartment located in a crowded steampunk city. He wears several layers of eyewear and has an odometer-like counter in his forehead which runs forward and backward. Mr. Hublot also displays several OCD symptoms, such as turning the lights on and off several times before leaving the living room and meticulously straightening the pictures on his wall.