In deep space, a race of gelatinous creatures abandon their dying world. Pushed through space by the solar wind, they make their way to Earth and land in San Francisco. Some fall on plant leaves, assimilating them and forming small pods with pink flowers. Elizabeth Driscoll (Brooke Adams), an employee at the San Francisco Health Department, is one of several people who bring the flowers home. The next morning, Elizabeth's boyfriend, Geoffrey Howell, DDS (Art Hindle), suddenly becomes distant, and she senses that something is wrong. Her colleague, health inspector Matthew Bennell (Donald Sutherland), suggests that she see his friend, psychiatrist Dr. David Kibner (Leonard Nimoy). While driving to a book party Kibner is attending, they are accosted by a hysterical man (Kevin McCarthy, in a direct homage to the original film). The man runs off, and is soon seen dead, surrounded by a crowd of emotionless onlookers. At the party, Matthew calls the police about the incident, and finds them strangely indifferent. An agitated party attendee starts declaring that her husband is not her real husband. Kibner works to reconcile them. He also suggests that Elizabeth wants to believe that Geoffrey has changed because she is looking for an excuse to get out of their relationship.
The film follows the cast of a once-popular television space-drama series called Galaxy Quest. The fictional series starred Jason Nesmith (Allen) as the commander of a spaceship called the NSEA Protector, Alexander Dane (Rickman) as the ship's alien science officer, Fred Kwan (Shalhoub) as the chief engineer, Gwen DeMarco (Weaver) as the computer officer and Tommy Webber (Mitchell) as a precocious child pilot. Guy Fleegman (Rockwell) played an unnamed security officer, who was quickly killed off in his only appearance on the show.
On the planet Krypton, using evidence provided by scientist Jor-El, the Ruling Council sentences three attempted insurrectionists, General Zod, Ursa, and Non, to "eternal living death" in the Phantom Zone. Despite his eminence, Jor-El is unable to convince the Council of his belief that Krypton will soon be destroyed when its sun explodes. To save his infant son, Kal-El, Jor-El launches a spacecraft containing him toward Earth, a distant planet with a suitable atmosphere, and where Kal-El's dense molecular structure will give him superhuman powers. Shortly after the launch, Krypton is destroyed.
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.
Dr. Jumba Jookiba is arrested and put on trial by the Galactic Federation for "illegal genetic experimentation", as evidenced by his Experiment 626, a living creature which is capable of creating untold chaos. Jumba is imprisoned while Experiment 626 is supposed to be exiled on a desert asteroid. 626 manages to escape in a spaceship and activates the hyperdrive, causing its guidance systems to malfunction and randomly set a course for Earth. The Grand Councilwoman dispatches Jumba and Agent Pleakley, the Council's Earth expert, to the planet to have 626 captured discreetly. 626 lands on the Hawaiian island of Kauaʻi, but is knocked unconscious by a passing truck and taken to an animal shelter.
A series of strange abductions have occurred in Gotham City, Central City, Coast City and Metropolis among others. Video footage suggests that Batman, a wanted, costumed vigilante, is behind the incidents. When a mysterious, burly, cloaked kidnapper abducts a woman, Green Lantern (Hal Jordan) arrives to confront the kidnapper and saves the woman when she is dropped from above. Green Lantern then attacks the kidnapper, revealing it to be a monstrous Parademon. The creature defeats Green Lantern soundly, and as he is about to be killed, Batman appears and attacks the Parademon, trying to interrogate it. The Parademon then attacks both heroes. They escape from the city's police and chase the creature into the sewers, where it charges a Mother Box and explodes. Batman and Green Lantern examine the box, deduce that it is of extraterrestrial origin, and decide to ask Superman for an answer. Another Mother Box, supplied by The Flash (Barry Allen) is being studied at S.T.A.R. Labs. Doctor Silas Stone, father of Vic Stone, deliberately misses his son's football game so he can study the box. Arriving in Metropolis, Batman and Green Lantern fight Superman—who has fought a Parademon previously and believes the heroes are working with it. The battle spreads over a portion of the city; it finally stops when Batman calls Superman "Clark". Superman uses his x-ray vision and recognizes Batman as billionaire Bruce Wayne. The three heroes then begin to collaborate. On planet Apokolips, Darkseid orders Desaad to begin an invasion of Earth in response to the superheroes' discovery of his plans.
In an alternate universe where evil usually triumphs over good and where the roles of the heroes and villains are reversed from their counterparts in the mainstream DC Universe, heroic analogues of Lex Luthor and the Joker (called the Jester) are attempting to steal a device, the "Quantum Trigger", from the headquarters of the Crime Syndicate. The pair trip an alarm but manage to secure the device. The Jester sacrifices himself to allow Luthor to escape and kills J'edd J'arkus and Angelique (alternate versions of Martian Manhunter and Hawkgirl respectively) with a radioactive bomb. Luthor is confronted by the remaining Syndicate members (Ultraman, Superwoman, Power Ring, Johnny Quick and Owlman) but escapes to the Earth of the heroic Justice League by activating a dimensional travel device.
In 2286, a large cylindrical probe moves through space, sending out an indecipherable signal and disabling the power of ships it passes. As it takes up orbit around Earth, its signal disables the global power grid and generates planetary storms, creating catastrophic, sun-blocking cloud cover. Starfleet Command sends out a planetary distress call and warns starships not to approach Earth.
Agent K and his partner Agent D intercept a truck smuggling illegal immigrants into the United States. Inside they discover an alien disguised as a human. When he runs, they shoot him and use neuralyzers to wipe the memories of the border patrol witnesses. D decides to retire and asks K to wipe his memory too. In upstate New York, an alien crash-lands and kills an abusive farmer named Edgar to use his skin as a disguise.
In the 23rd century, Earth has become a space-faring federation. While colonizing new planets, humans have encountered an insectoid species known as Arachnids or "Bugs", with their home being the distant world Klendathu. The bugs appear to be little more than killing machines, though there are suggestions that they were provoked by the intrusion of humans into their habitats.
Batman (Clark Bartram) corners an escaped Joker (Andrew Koenig), only to have the villain suddenly dragged off by an Alien. The Alien is, in turn, killed by a Predator, which Batman fights and defeats. Other Predators then appear just as more Aliens emerge from the darkness behind Batman. The film ends abruptly with Batman caught in between the two alien species.
While no cohesive plot is apparent from the vignette style of the trailer, it can be pieced together that Batman has been murdered, and his killer remains at large. Dick Grayson, long since retired from his superhero days and married to Barbara Gordon with a child, decides to resume his crime-fighting days as Robin; Remarkably, Grayson does not take up the Nightwing identity. The filmmakers said they chose this because many people outside the comic book community are unfamiliar with Nightwing and they wanted to appeal to a wider audience.
Clark Kent and Lois Lane exit the Daily Planet building with Lois asking Clark why he always runs to the bathroom whenever a big story breaks. He explains to her that his bladder goes out of control whenever he gets nervous. Suddenly, a giant robot appears from out of nowhere and attacks Metropolis. Clark quickly disappears into a nearby phone booth and changes into Superman to combat the robotic threat. After a brief battle, Superman throws the robot into the air, only to see armies of dozens of robots flying in the sky.
In 2005, Unicron, a roaming artificial planet, devours robot planet Lithone. Elsewhere, the evil Decepticons control the Transformers' homeworld, Cybertron. The heroic Autobots are using two of Cybertron's moons as staging areas, preparing to strike against the Decepticons. In need of energon cubes, an Autobot shuttle is readied for launch to Autobot City on Earth. The Decepticons ambush the shuttle, killing Brawn, Prowl, Ratchet and Ironhide, intending to use the ship to infiltrate Autobot City.
As a Klingon moon, Praxis, explodes without warning, the starship USS Excelsior, commanded by Captain Hikaru Sulu, is struck by the shock wave and its crew discovers that much of the moon has been obliterated. The loss of their key energy production facility and the destruction of the Klingon homeworld's ozone layer throws the Klingon Empire into turmoil. No longer able to maintain a hostile footing, the Klingons sue for peace with their longstanding enemy, the United Federation of Planets. Accepting the proposal before the Klingons revert to a more belligerent approach, Starfleet sends the USS Enterprise-A to meet with the Klingon Chancellor, Gorkon, and escort him to negotiations on Earth. Enterprise 's captain, James T. Kirk, whose son David was murdered by Klingons years earlier, opposes the negotiations and resents his assignment.