Between 1978 and 1982, the adventures of the crew of the NSEA Protector were viewed by enthusiastic audiences of the television series Galaxy Quest. Eighteen years later, the stars of the show have been reduced to convention appearances and store grand-openings. Most of the cast members are variously resentful, embittered, jealous or resigned. The only cast member who derives any sort of pleasure from the adoration of the doting fans is Jason Nesmith, the egomaniacal star and "commander" of the crew, who laps up their continuing devotion. However, Nesmith overhears certain comments that make him realize that non-fans consider him a has-been and a joke and that his co-stars badmouth him behind his back.

At one convention, Jason is approached to discuss what he assumes to be a personal appearance in an amateur episode by a slightly weird group of fans. They send a limousine to pick him up the next day, as he requested. Jason is impressed by the high production values of their starship "set," which are unusual for an amateur effort. Jason steps into his role as Captain, and summarily orders his crew to fire upon the "evil alien overlord" Sarris, who appears on the Bridge viewscreen. When he asks to go home, he is sent through interplanetary space in a gelatinous transportation pod. Only then does he realize that he really was in outer space. It is revealed that Mathesar (Enrico Colantoni) and the others are Thermians, a peaceful, naïve, cephalopod-like alien race who, having received twenty-year-old transmissions of Galaxy Quest (as well as other shows such as Gilligan's Island) from Earth, and having no concept of fiction, have interpreted the show as "historical documents." They have structured their entire society around the "teachings" of the series, going so far as to build an exact replica of the Protector. Special devices allow them to appear in human form, though their speech and mannerisms are never quite human.

Jason loves the idea of being regarded as a hero by a bona fide alien race and therefore recruits his reluctant fellow actors into joining him as his "crew." In the process of rushing to find them, he accidentally exchanges the communicator the Thermians gave him with a toy version of it held by an avid young fan of the show named Brandon. Unfortunately, just as the new Protector is real, so is Sarris, a ruthless reptilian warlord engaged in a genocidal war of annihilation against the Thermians. The actors, in order to help the Thermians, must fulfill their television roles. In return for the Thermians' safety, Sarris demands the "Omega 13," a device the Thermians built in the bowels of the Protector, again copied from the show. Unfortunately, the Omega 13 was used only in the cliffhanger at the end of the series' final episode, which had no sequel. Its function is unknown.

After a battle against Sarris and his crew, the Thermian Protector is heavily damaged by space mines leftover from an earlier war. A new Beryllium sphere is needed to revive the main power systems. The crew land on an alien planet, where they evade a group of fierce goblin-like blue aliens in order to retrieve the hollow sphere. Jason, who is last in the line of escape, is accidentally left behind. The small blue aliens invoke a monster formed of animated rocks to kill him. He evades the monster and is ultimately beamed out using the Protector's Digital Conveyor (an obvious homage to the Star Trek transporter device).

Unfortunately, while most of the characters were preoccupied with rescuing Jason from the alien planet, the ship was overrun by Sarris and his soldiers. Jason tries to save his fellow actors by admitting that the television series Galaxy Quest was a mere fiction, which has to be explained to the honest Thermians as "deception." Sarris is most amused, since his genocidal war against the Thermians was largely precipitated by their resistance -- based on the "teachings" of the TV program. He orders the Protector's reactor to be set to overload, the air to be let out of the room the Thermians are confined in, and the actors to be expelled into space. The actors, using a clever ruse taken from an episode of the show, are able to fool their dim-witted guards and escape. The crew then embark to rescue the Thermians and destroy Sarris: Jason and his fellow actor Gwen DeMarco move to stop the core from detonating, while Alexander and the Thermian Quellek attempt to save the rest of the Thermians; Fred and his ersatz sidekick Guy Fleegman defeat Sarris' soldiers, and Tommy Webber, who had played the pilot in their television series, takes over the ship's controls.

Jason is able to contact Brandon (who has a genuine Thermian communicator, due to an accidental exchange happened during Jasons' first "comeback" from Outer Space) and his nerdy friends, who have a ridiculous amount of knowledge of the ship. Brandon guides Jason and Gwen through the Protector's dangerous inner systems and thence to the core's control center. En route, Brandon reveals that the Omega 13 will either destroy the known universe or send the user back in time 13 seconds - enough time to change one mistake. They cannot seem to shut down the reactor, but the timer (true to the show) shuts off by itself with only one second to spare.

Meanwhile, Alexander and Quellek complete their mission by rescuing the Thermians from asphyxiation. Quellek is subsequently killed by one of Sarris' soldiers, and the grieving Alexander reverently quotes his character's oath of vengeance, which he had grown to loathe over the years.

After the crew save the Thermians and free the ship, they confront Sarris again. As before, the Protector is pummeled by Sarris' mighty flagship; Jason, anticipating the fight, orders Tommy to fly near the mines, which home in on and begin to follow the speeding Protector. The Protector then flies straight toward Sarris' ship, in a game of "chicken." Jason, at the last available moment, orders evasion; the many mines following the Protector lock onto Sarris' mighty ship, destroying it.

As the humans return to the command deck to celebrate their victory. Sarris, disguised as Fred, enters the control cabin and begins shooting the crew. Most are killed; but before Sarris can finish the job, Jason orders Mathesar to "activate the Omega 13," which sends him back 13 seconds in time. Jason attacks the disguised Sarris and strips him of his gun. When Sarris reveals a knife, Mathesar knocks him out.

The ship is out of control, and the humans separate the command deck from the ship to make a forced landing on Earth. It crashes into a parking lot, through the side of a building and onto the stage of a Galaxy Quest convention, where fans await the missing actors. The crew step one by one onto a stage, where they face their adoring fans. Sarris emerges behind them, whereupon Jason anticlimactically disintegrates him, to thunderous applause. The remaining Thermians fly away to rebuild their civilization. Laliari stays behind in order to live with Fred, from whom she cannot bear to be parted.

Some time later, the crew of the Protector star in a sequel of Galaxy Quest, called Galaxy Quest: the Journey Continues. Laliari and Guy, as well as the rest of the actors, assume prominent roles. The film ends as the Protector zooms off into outer space once more.

Note: The plot echoes two fan fiction stories: "Visit to a Weird Planet", or the inside story behind the antagonism of a certain network toward a certain segment of the population" by Jean Lorrah and Willard F. Hunt and "Visit to a Weird Planet, Revisited" by Ruth Berman. In both of these stories the plot device includes a misadventure of the Star Trek-series actors (Shatner, Nimoy, and Kelley) when they are inadvertently beamed into the real U.S.S. Enterprise -- exchanging places with the 'real' Kirk, Spock and McCoy who are simultaneously transported to the set of the Star Trek series.

I had originally not wanted to see Galaxy Quest because I heard that it was making fun of Star Trek and then Jonathan Frakes rang me up and said 'You must not miss this movie! See it on a Saturday night in a full theatre.' And I did and of course I found it was brilliant. Brilliant. No one laughed louder or longer in the cinema than I did, but the idea that the ship was saved and all of our heroes in that movie were saved simply by the fact that there were fans who did understand the scientific principles on which the ship worked was absolutely wonderful. And it was both funny and also touching in that it paid tribute to the dedication of these fans. -- Patrick Stewart Source

I think it's a chillingly realistic documentary [laughs]. The details in it, I recognized every one of them. It is a powerful piece of documentary filmmaking. And I do believe that when we get kidnapped by aliens, it's going to be the genuine, true Star Trek fans who will save the day. ... I was rolling in the aisles. And [star] Tim Allen had that Shatner-esque swagger down pat. And I roared when the shirt came off, and [co-star] Sigourney [Weaver] rolls her eyes and says, 'There goes that shirt again.' ... How often did we hear that on the set? [Laughs.] - George Takei Source

Usually, as in the case of Star Trek, when there is an explosion, the camera would tilt to one side and the actors would fall to the other, creating the visual effect of the set rolling and the actors reacting (an effect often called the Irwin Allen rock-and-roll by film buffs). However, the Protector bridge set was built on hydraulic rams (or 'gimbals'), so when an explosion supposedly occurred, the set would actually (and very suddenly) rock to one side, vibrate wildly and throw the actors out of their seats. According to interviews on the DVD release of the film, the effect was so real that it actually frightened (and injured) several of the main cast. Although not used in Star Trek series or movie productions at the time Galaxy Quest was made, the technique was finally employed for the tenth Trek movie, Star Trek Nemesis, though many reviews of that film still made reference (erroneously) to the supposedly 'fake' visual effect as it appeared onscreen.