Giant unidentified lifeforms known as S-Class Species begin appearing across Japan, posing an escalating threat that existing military forces struggle to contain. In response, the Japanese government establishes a specialized task force called the S-Class Species Suppression Protocol, or SSSP, bringing together experts from various fields to analyze and combat these creatures. The team includes the analytical yet reserved Shinji Kaminaga, a former police officer assigned as the operations planner, and the sharp-witted Hiroko Asami, an analyst who becomes his reluctant partner.

During a confrontation with one such kaiju, Kaminaga is killed. At that moment, a towering silver humanoid being descends from beyond Earth's atmosphere to defeat the creature. This alien entity, codenamed Ultraman by the government, chooses to atone for his arrival by merging with Kaminaga, taking on his human form to live among the population while protecting the planet from further threats. As Ultraman, he possesses immense strength, the ability to fly, and a devastating energy attack known as the Specium Ray. The SSSP continues its mission, now with Kaminaga secretly capable of transforming into the giant hero when needed, while his partner Asami gradually uncovers his true nature.

The appearance of Ultraman draws the attention of other extraterrestrial forces. The alien Zarab arrives on Earth, seeking to exploit the situation for conquest. Zarab captures Kaminaga and reveals his identity as Ultraman to the world, then impersonates the hero to commit acts of destruction in an attempt to turn humanity against him. With Asami's help, Kaminaga escapes and defeats Zarab, but his exposed identity leaves him without a place in human society.

A more sophisticated alien named Mefilas then makes contact with the Japanese government. He demonstrates a technology called the Beta System, which can artificially enlarge living beings, by using it on a kidnapped Asami and returning her to normal size. Mefilas proposes granting this technology to humanity as a means of self-defense against hostile aliens, but his true goal is to establish himself as a superior authority over Earth, placing humanity under his control. When Kaminaga as Ultraman refuses Mefilas's offer of alliance, a battle ensues. Mefilas gains the upper hand but ultimately withdraws after sensing the arrival of another being from Ultraman's home world.

This new arrival is Zoffy, a high-ranking commander from the Land of Light in Nebula M78. Zoffy delivers devastating news. Because Ultraman has merged with a human, the knowledge of the Beta System has spread across the cosmos, leading other civilizations to view humanity as a potential weapon that must be eliminated. Zoffy deploys Zetton, a planet-destroying biological weapon, into Earth's orbit with the power to annihilate the entire solar system. Ultraman attempts to destroy Zetton alone but is soundly defeated and reverts to Kaminaga, falling into a coma.

Facing annihilation, the SSSP discovers that Kaminaga left behind a USB drive containing the fundamental principles of the Beta System. Led by physicist Takumi Taki, scientists from around the world collaborate on a desperate plan. By inverting the Beta System, they can create a dimensional rift to send Zetton into another dimension. The plan requires Ultraman to act as the catalyst, which will likely result in him being pulled into the rift as well, never to return. Despite the SSSP commander Kimio Tamura's hesitation, Kaminaga accepts the sacrifice. He transforms into Ultraman one final time and successfully executes the plan, disappearing into the void as Zetton is banished.

In the aftermath, Zoffy appears to Ultraman as he drifts through another dimension. Impressed by humanity's intelligence and determination, Zoffy announces that the destruction order has been rescinded. He offers to take Ultraman back to their home world, but Ultraman, having grown to care for Earth and its people, refuses. He asks Zoffy to separate him from Kaminaga, giving the human his life back. Zoffy agrees, and Kaminaga awakens on Earth, greeted by his comrades in the SSSP with no memory of his time as Ultraman.