In UC 0093, Char Aznable has returned to lead Neo Zeon. As the film opens, Char’s forces have arranged to drop the asteroid Fifth Luna on the Earth. Special task force Londo Bell, whose members include veteran soldiers Amuro Ray and Bright Noa, attempt to prevent the catastrophe. Char is successful and the asteroid crashes into Lhasa, Tibet.
Earth Federation Prime Minister Adenaur Paraya and his teenage daughter Quess narrowly escape the crashing asteroid. Their space shuttle meets with Londo Bell’s command ship, the Ra Cailum, which has just finished collecting Amuro’s new mobile suit, the RX-93 Nu Gundam, and Amuro’s close friend Chan Agi. The Nu Gundam is equipped with new “psycho-frame” technology, which amplifies Newtype abilities. Bright is reunited with his young son Hathaway, who was also on the escaping shuttle. Adenaur instructs Bright to deliver him to the colony Londenion for some important business. While on board, Quess becomes smitten with Amuro, and Hathaway develops a crush on Quess.
On the Londenion colony, Adenaur’s business is revealed to be a secret meeting with Char and other Neo Zeon leaders to arrange a treaty; the Neo Zeon will gain the asteroid Axis in exchange for disarming their fleet. While relaxing on the colony with Quess and Hathaway, Amuro recognizes Char and confronts him. Overhearing the two men argue, Quess becomes enamored of Char’s philosophies and leaves the colony with him, much to Hathaway’s distress.
Quess turns out to be a Newtype and a naturally talented mobile suit pilot. Char takes advantage of her unstable nature and manipulates her feelings to use her as a weapon against Amuro. Char reveals that the treaty with the Federation is a ruse. The Neo Zeon forces ambush the Federation fleet at the supposed disarmament, and Axis is sent on a collision course with the Earth. Londo Bell attempts to stop the asteroid using Axis’ stockpile of nuclear weapons, but only succeeds in splitting the asteroid into two pieces.
A furious battle between Londo Bell, the Federation, and Neo Zeon erupts. Quess descends into madness and violence while piloting the psycho-frame-equipped mobile armor Alpha Azieru. Hathaway steals a mobile suit and futilely tries to convince Quess to stop fighting and come with him. Chan kills Quess to protect Hathaway from the girl’s insane attacks but is herself killed by Hathaway in a rage over Quess’s death. Amuro and Char duel in their psycho-frame mobile suits, the Nu Gundam and MSN-04 Sazabi, and Amuro defeats his long-time rival. With Char’s escape pod in tow, Amuro desperately attempts to push back the descending Axis asteroid, aided by Federation and Zeon suits alike. The power of the Nu Gundam’s psycho-frame amplifies Amuro’s Newtype abilities to an unbelievable level. Amuro, Char, and the Nu Gundam vanish in a massive flare of light as both halves of Axis are pushed away from the Earth.