Having emerged victorious from his confrontation with Ultraman Zero in the prior film, the malevolent Ultraman Belial has rebranded himself as Galactic Emperor Kaiser Belial. His ambitions for universal domination have now escalated, bolstered by the support of two formidable allies and the creation of numerous robotic minions called Legionoids and Darklops. With his newfound power, Belial sets his sights on the planet Esmeralda, where he successfully defeats the Esmeraldan Royal Guard (the battle occurs off-screen) and captures the planet, ultimately brainwashing its guardian in the process.
Meanwhile, in Nebula M78, the Land of Light engages in a defense against an attack by one of Belial’s robotic carriers, which is transporting three Darklopses. Fortunately, Ultraman Zero, alongside Ultraseven, intervenes, destroying the Darklopses before they can escape. Upon tracing the energy signature of the Darklopses, they deduce that these foes originate from an alternate universe, complicating their ability to unite against the threat. Resolute in his mission, Ultraman Zero decides to confront Belial alone. The Ultra Brothers construct a travel sphere to send him to the universe under Belial’s terror. As a parting gift, Ultraseven presents Zero with the Ultra Zero Bracelet, a crucial device that serves as an emergency power source, usable three times in dire circumstances.
In the universe of Planet Annu, Belial’s Legionoid army wreaks havoc while a group of rebels attempts to fight back. Among the rebels are Run and Nao, two brothers operating a vehicle to engage in combat. When Run risks his safety to save Nao from falling into a volcanic pit, Ultraman Zero arrives just in time, empowered by the Ultra Zero Bracelet to confront the Legionoids. Faced with dwindling energy due to the suns of that universe being unable to recharge his powers, Ultraman Zero resorts to using Run’s body as a host, allowing him to easily defeat the army, but at the cost of adopting Run’s identity to keep him safe and conserve energy.
After introducing himself to Nao as "Run," Zero learns of Kaiser Belial's plans to harvest energy from emeralds found throughout the universe. Nao insists that only an artifact known as the Shield of Baradhi can thwart Belial. Their conversation is cut short when they face another assault from the Legionoids. In their desperate bid for survival, they stow away on a ship named Jean-Bird, which is revealed to be sentient and has deep ties to the royal family of Esmeralda. Here, they encounter Princess Emerana, who becomes a close ally after Run discloses his true identity as Ultraman Zero.
Determined to thwart Belial's conquest, the trio and Jean-Bird set off in search of the mythical Shield of Baradhi. They soon encounter the Pirates of Flames, a notorious crew led by the fiery Glenfire. Initially met with hostility, Ultraman Zero transforms and proves his intentions, leading to a battle where Zero demonstrates his strength. The fight ends in a standstill, and Zero gains the pirates' trust. However, their celebration is short-lived as they are ambushed by Belial’s Legionoids, commanded by the fierce general Darkgone. In the ensuing chaos, Glenfire uses his fire abilities to ignite Space Nitromethane, creating a massive explosion that obliterates the Legionoids, but seemingly claims Glenfire's life.
After securing the location of the Shield of Baradhi, the heroes venture to the 2-D Planet of Mirrors, where they confront Mirror Knight, who has fallen under Belial's corrupt influence. In an intense battle, Ultraman Zero redeems Mirror Knight, expelling the dark energy controlling him. Now restored, Mirror Knight joins the quest, revealing that the shield lies beneath the planet's surface.
As they finally reach the Shield of Baradhi, it becomes apparent that time has ravaged this ancient artifact, reducing it to sand right before their eyes, a heartbreaking moment for the team as they feel their efforts amount to nothing. Suddenly, their spirits are crushed further when Iaron, another general of Belial, attacks and begins to destroy the Planet of Mirrors. In the chaos, the heroics of Mirror Knight are tested, and Run finds himself unconscious after attempting to transform into Ultraman Zero once more.
Upon awakening, Run faces the wrath of Kaiser Belial aboard a colossal ship anchored to Esmeralda. Belial taunts Run as he watches in horror; the Ultras struggle against the onslaught of Darklopses. However, it’s a relief to discover that both Nao and Emerana have survived the destruction. Moreover, Mirror Knight makes a triumphant return to rescue Run, facilitating his transformation into Ultraman Zero.
The climactic showdown occurs as Ultraman Zero battles Kaiser Belial. The two clash intensely, yet Belial unleashes a Deathcium Ray, incapacitating Zero and making his escape. Meanwhile, a simultaneous fight unfolds as Mirror Knight encounters Iaron, and Jean-Bird faces Darkgone. In a selfless act, Emerana sacrifices her own energy to revive Jean-Bird, enabling it to transform into Jean-Bot. With collective efforts, they confront and eliminate their adversaries, but the situation grows dire when Kaiser Belial absorbs the energy of the emeralds, transforming into the monstrous Arch Belial.
Now a towering behemoth, Arch Belial relentlessly overpowers Ultraman Zero, while Mirror Knight and Jean-Bot find themselves outmatched. Just as hope dims, Glenfire miraculously reappears, having survived, along with the reinforcements from the Planet of Mirrors and the Esmeraldan royal guard. They join forces against Belial’s armies, but the threat escalates when Arch Belial readies his Arch Deathcium Ray to wipe out Zero and Esmeralda.
Ultimately, after exhausting his strength, Ultraman Zero succumbs to his battles. However, Nao reminds everyone not to lose hope. In a miraculous twist, Ultraman Noa grants Zero renewed life and the Shield of Baradhi, transforming him into Ultimate Zero. With his newfound powers, Zero annihilates Arch Belial using the Final Ultimate Zero, thus liberating the universe from his tyranny.
With the defeat of Belial, peace is restored. Princess Emerana emerges, having survived, using her energy to empower Jean-Bot. The Ultras in M78 are revealed to have successfully thwarted Belial's forces as well. Ultraman Zero separates from Run’s body, allowing him to lead a peaceful life alongside Nao once again. Yet, moved by the bonds formed throughout their adventure, Ultraman Zero decides to stay, assembling the Ultimate Force Zero from his friends and allies, embracing the unknown future ahead.
