Once, the Space Revolutionary Army (SRA) waged a war of independence against the United Nations Earth Forces (UNEF). Eight months into the war, the SRA threatened to launch multiple Colony Drops against Earth unless the UNEF surrendered unconditionally. The UNEF responded by deploying their ultimate weapons, the Gundam mobile suits. However, the Gundams were insufficient to stop the SRA from dropping seemingly every space colony on Earth, eradicating the vast majority of humanity.
The year is After War 0015. Although Earth's environment has recently stabilized, society has yet to be rebuilt. In one of the few surviving cities, a pair of hustlers calling themselves the Red Bi-stars claim to be veterans of the war as well as Newtypes, humans who have evolved to gain psychic powers. Suddenly, a bandit piloting a Jenice attacks the city. The Bi-stars run off and are promptly blown away by the bandit. While the city-dwellers put up a fight, the battle seems to be lost until a teenager named Garrod Ran fires a flashbang at the Jenice's main camera, uses a grappling hook to reach the cockpit while the pilot can't see outside, and hold the bandit at gunpoint. Garrod throws the bandit to the vengeful city dwellers and captures the Jenice so he can sell it.
A man named Rike Anto is impressed and offers Garrod a job. Rike wants Garrod to rescue Tiffa Adill, a teenage girl who was recently kidnapped by a gang of Vultures, scavengers who seek pre-war relics to sell.
On the Vulture ship, Freeden, Captain Jamil Neete instructs his subordinates Sara Tyrell, Toniya Marme, and Shingo Mori to mind the bridge while he checks on Tiffa, who is currently asleep. None of the crew knows why Jamil has taken Tiffa, but they trust him. Tiffa dreams of being grabbed by a Gundam X. When she wakes up, she stares at the moon.
Garrod sneaks on board the Freeden while the ship's crew are distracted by refilling their water stockpiles from a lake. He takes a detour to Jamil's quarters to find valuables to steal, but the only thing he finds is a mobile suit control unit. Garrod finds Tiffa, who agrees to come with him because she has been waiting for him.
Garrod and Tiffa flee the Freeden in a buggy. The Freeden attempts to pursue, but they are stopped when a rival Vulture gang attacks them. Garrod and Tiffa rendezvous with Rike, but Garrod notices that the sight of Rike is sending Tiffa into a panic attack and flees with her. Rike and his subordinates respond by attacking Garrod in Daughtress mobile suits, but Tiffa is able to predict their attacks and helps Garrod to dodge them. Tiffa tells Garrod that she knows where he can find power. Tiffa guides Garrod to an abandoned UNE mobile suit factory, which contains a Gundam X in perfect condition. Garrod and Tiffa get into the Gundam, which is lacking a control unit. On a whim, Garrod inserts the control unit he stole from Jamil into the Gundam and it activates. Garrod quickly kills Rike and his minions with his new Gundam. Suddenly the Freeden arrives with two mobile suits: the Gundam Airmaster, piloted by the mercenary Witz Su, and the Gundam Leopard, piloted by the mercenary Roabea Roy. Jamil asks his crew if the moon is out and the camera pans up to show that it is.
- Chekhov's Gun: The mobile suit control unit Garrod steals from Jamil, which turns out to be the key to activating the Gundam X.
- Downer Beginning: The prologue ends with most of humanity dead.
- The Dulcinea Effect: Garrod is willing to abandon a lucrative job simply because he realizes that it will harm a girl that he barely knows.
- Hit So Hard, the Calendar Felt It: The calendar was reset after the apocalyptic ending of the previous war.
- Mythology Gag:
- Scary Shiny Glasses: Rike's glasses become opaque from the lighting after his true intentions towards Tiffa are revealed.
- Title Drop: Every episode of Gundam X is named for a quote from that episode. This episode's title is Jamil's question to his crew at the end.