In UC 0093, the enigmatic figure of Char Aznable (Shûichi Ikeda) has re-emerged, now leading the formidable Neo Zeon army against the Earth Federation. Char is driven by a fervent belief that humanity cannot achieve true freedom without severing ties with Earth and evolving into a New Type of mankind. The film begins with Char's forces launching a dire plan: to drop the Fifth Luna asteroid onto Earth to induce a catastrophic nuclear winter. In response, a special task force known as Londo Bell, which includes seasoned veterans like Amuro Ray (Tôru Furuya) and Bright Noa (Hirotaka Suzuoki), engages Neo Zeon in a desperate struggle to avert disaster.
The rivalry between Char and Amuro, which dates back to the One Year War in 0079, is reignited as both pilots take to their mobile suits. Amuro commands the RGZ-91 Re-GZ, a later iteration of the Zeta Gundam, while Char pilots the imposing MSN-04 Sazabi, a machine enhanced with psycho-frame technology that amplifies Newtype abilities. Despite Amuro's impressive skills, he finds himself outmatched and ultimately retreats as the asteroid hurtles toward Earth, on a collision course with Lhasa, Tibet.
On the ground, the Earth Federation's Vice Minister Adenauer Paraya (Trevor Devall) and his rebellious daughter Quess (Maria Kawamura) scramble to evacuate. As they try to board an evacuation shuttle, Bright Noa's family is shamefully denied their seats by the self-serving Prime Minister. In a heart-wrenching decision, Mirai, Bright's wife, chooses to send their son Hathaway Noa (Nozomu Sasaki) aboard the shuttle, knowing they must escape the impending doom while leaving behind her other child.
As events unfold, Amuro heads to intercept the asteroid's trajectory with his new mobile suit, the RX-93 ν Gundam, designed specifically for him and equipped with the psycho-frame technology. This new suit is engineered by his ally, Chan Agi (Mitsuki Yayoi), who expresses concern over the origins and potential implications of the technology. Meanwhile, tensions rise as Quess develops feelings for Amuro, unaware of her latent Newtype abilities that Char exploits for his own gain.
At a critical meeting on the Londenion colony, the Vice Minister reveals a deceptive peace treaty with Char, masking a sinister maneuver to gain control over the asteroid, Axis. Amidst the tranquil colony, the atmosphere shifts dramatically when Amuro confronts Char, leading him to draw a gun. However, Quess intervenes, drawn to Char's charisma, and interrupts their skirmish, which only intensifies the psychological warfare at play. Char manipulates Quess's emotions, eager to harness her powers as a Newtype for his ambitions.
As battle erupts, Quess, piloting an MSN-03 Jagd Doga, unwittingly becomes part of Neo Zeon's ambush against the Federation fleet, resulting in disastrous consequences. Overwhelmed by her father's demise and her newfound capabilities, Quess spirals into chaos, while Hathaway disobeys his father's orders. He stows away in an unarmed mobile suit, determined to save her and confront the unfolding disaster.
In a series of fierce confrontations, Bright leads the Londo Bell forces against Char's overwhelming might in a valiant effort to prevent Axis from descending upon Earth. They deploy tactical strategies to intercept the asteroid, with Bright bombarding it with missiles containing nuclear warheads. As the battlefield rages on, the truth of Char’s treachery prevails, revealing the catastrophic stakes at play.
The climax leads to a rematch between Amuro and Char, where past grievances surface, enveloping them in a shroud of emotion and unresolved tension, notably invoking memories of Lalah Sune, lost during the One Year War. In a dramatic climax, Amuro gains the upper hand, but not without devastating costs. With Axis on a direct collision course with Earth, the stakes reach their zenith as Amuro and Char face off amidst the debris of their ambitions.
Desperation fuels Amuro's actions as he harnesses the collective will of humanity in a last-ditch effort to avert disaster. The discussions of motivations and past losses flow with fervor, as Char derides his former rival, and with the help of combined psychic energies, Amuro and the remaining pilots defy the odds. Their collective strength momentarily sways the dual halves of Axis from their catastrophic trajectory — but at what cost?
In the aftermath, as peace appears tentative yet achievable, Hathaway and the rest of humanity witness the spectacle of a brilliant aurora in the sky, a reminder of what was fought for and the uncertain future that lies ahead.
