In the year 2293, retired Captain James T. Kirk, Montgomery Scott, and Pavel Chekov attend the maiden voyage of the Federation starship USS Enterprise-B, under the command of the unseasoned Capt. John Harriman. During the voyage, Enterprise is pressed into a rescue mission to save two El-Aurian ships from a strange energy ribbon. Enterprise is able to save some of the refugees before their ships are destroyed, but the starship becomes trapped in the ribbon. Kirk goes to deflector control to alter the deflector dish, allowing Enterprise to escape, but the trailing end of the ribbon rakes across Enterprise 's hull, exposing the section Kirk is in to space; he is presumed dead.
Telly Paretta (Julianne Moore) believes that her son, Sam (Christopher Kovaleski), died fourteen months ago in a plane crash, but her husband Jim (Anthony Edwards) tells her that she's delusional and that they have never had a son, and Eliot (Jessica Hecht) doesn't appear to believe in Sam's existence despite her closeness to him. Dr. Munce (Gary Sinise) tells her that Sam was merely a figment of her imagination and is just imagining a life that might have been. He recommends that she be sent to a hospital, but she runs away and meets with a man named Ash (Dominic West) who she thinks is the father of a girl (Kathryn Faughnan) who was friends with her son and died in the same crash. At first he dismisses her, claiming he never had a daughter, and calls the police. After she is taken into custody, however, he remembers his daughter and rescues Telly. Together they escape and go into hiding, pursued by National Security agents.
During the SETI program, Earth's scientists send out transmissions (shown to be the Arecibo message) with information about Earth and its inhabitants, DNA structure, etc., in hopes of finding life beyond Earth. They then receive transmissions from an alien source on how to create endless fuel effortlessly. Therefore, the scientists assume that this is a friendly alien species. From a second alien transmission, the scientists receive information about an alien DNA along with instructions on how to splice it with human DNA. A government team led by Xavier Fitch (Ben Kingsley) goes forward with the genetic experiment attempting to induce a female, because a female would have "more docile and controllable" traits. One of the hundred experimental ova produces a girl named Sil, who looks like a normal human but develops into a 12-year-old in 3 months.
Lieutenant Commander Data (Brent Spiner) is temporarily transferred to an undercover mission observing the peaceful Ba'ku people. While on their planet, he malfunctions and reveals the presence of the joint Federation–Son'a task force observing the Ba'ku. Admiral Matthew Dougherty (Anthony Zerbe) contacts the USS Enterprise-E to obtain Data's schematics but adamantly states the presence of the Enterprise is not needed. Captain Picard decides to ignore these orders and takes the Enterprise to capture Data. After stopping Data, Captain Jean-Luc Picard (Patrick Stewart) becomes suspicious of Dougherty's insistence that the Enterprise is no longer needed. His crew investigates the cause of Data's malfunction. They discover that the Ba'ku are technologically advanced, but have rejected its use to live simpler lives. Due to unique radiation or "metaphasic particles" emanating from their planet's rings, they are effectively immortal. Dougherty's allies, the Son'a, are a decrepit race who use medical techniques to prevent death; their excessive use of cosmetic surgery gives them a mummified appearance. The Enterprise crew also begin to experience the rejuvenation effects of the planet: Lt. Commander Geordi La Forge (LeVar Burton) finds his eyes have regenerated and he no longer requires ocular implants; Commander William Riker (Jonathan Frakes) and Counselor Deanna Troi (Marina Sirtis) rekindle their long-abandoned relationship; and Picard develops a romantic relationship with the Ba'ku woman Anij (Donna Murphy).
Four waves of increasingly deadly attacks have left most of Earth decimated. Against a backdrop of fear and distrust, Cassie is on the run, desperately trying to save her younger brother. As she prepares for the fifth wave, Cassie teams up with a young man who may become her final hope – if she can only trust him.
On Planet 51, green humanoids with snail-like feelers and pointed ears live peacefully in a society reminiscent of 1950s America, but with alien technology and with 1950s-themed alien homes. In the town of Glipforg, Lem is a teenage boy with a new part-time job at the local planetarium and a long-time crush on his neighbor Neera. His best friend is Skiff, a big fan of the Humaniacs films. At a barbecue Neera's family is having, Lem tries to ask her on a date, but her hippie friend, Glar, keeps interrupting with his protest songs.
The commercial spacecraft Nostromo is on a return trip to Earth with a seven-member crew in stasis. Detecting a mysterious transmission, possibly a distress signal, from a nearby planetoid, the ship's computer, MOTHER, awakens the crew. Following standard company policy for such situations, the Nostromo lands on the planetoid and Captain Dallas, Executive Officer Kane, and Navigator Lambert head out to investigate. They discover the signal is coming from a derelict alien spacecraft. Inside, they find the remains of a large alien creature whose ribcage appears to have exploded from the inside.
The film begins with a Broadway-style number "So Long, and Thanks for All the Fish", sung by the dolphins of the world, who are aware of the Earth's impending doom. At the end, they all jump out of the oceans and into space, leaving Earth for good.
In Kentucky, a family watches an enormous horde of cattle running past their home, having caught fire, and a flying saucer leaving Earth. The ship explodes before it returns to Mars, and hundreds of other Martian ships leave Mars and head towards Earth.
Wayne Grey (Seann William Scott), a fireman trainee practicing in a shack in the desert near Glen Canyon, Arizona, sees a meteor strike his car and land in an underground cavern. College professor Ira Kane (David Duchovny) and his colleague, geology professor Harry Block (Orlando Jones), investigate, taking a sample of strange blue liquid that oozes from it. Ira discovers that it harbors extraterrestrial single-celled nitrogen-based organisms multiplying exponentially, condensing millions of years of evolution within a matter of hours. The next day, they take the science class to survey the meteor site and find it already surrounded by evolved oxygen-converting fungi and alien flatworms. Ira and Harry discover that the cells and organisms reproduce rapidly through mitosis after seeing one of the flatworms they collected in a jar split into another.
Major Alan "Dutch" Schaefer and his six-man team, consisting of himself, operators Mac Eliot, Billy Sole, and Blain Cooper, ordnance expert Jorge "Poncho" Ramírez and radioman Rick Hawkins, are tasked by the CIA with spearheading the rescue of an official held hostage by insurgents in Val Verde. Agent George Dillon, an old friend of Schaefer's, is assigned to supervise. The team is taken to a remote jungle and begins the mission.
Graeme Willy (Simon Pegg) and Clive Gollings (Nick Frost) are British comic book enthusiasts and best friends who travel to the United States to attend the annual San Diego Comic-Con International, and to take a road trip through the American Southwest to visit sites significant to UFO lore. While driving on a remote desert highway at night, Graeme and Clive observe a car driving erratically and then crash. They stop to investigate and offer assistance to the driver, who turns out to be an alien named Paul (voiced by Seth Rogen). Clive faints, but Graeme agrees to assist Paul and gives him a ride.
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.
In the year 2285, Admiral James T. Kirk oversees a simulator session of Captain Spock's trainees. In the simulation, Lieutenant Saavik commands the starship USS Enterprise on a rescue mission to save the crew of a damaged ship. When the Enterprise enters the Klingon Neutral Zone to reach the ship it is attacked by Klingon cruisers and critically damaged. The simulation is named the "Kobayashi Maru"—a no-win scenario designed to test the character of Starfleet officers. Later, Dr. McCoy joins Kirk on his birthday; seeing Kirk in low spirits, the doctor advises Kirk to get a new command and not grow old behind a desk.
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.