In The New '20s-era Japan, several large lifeforms begin to appear one after another, forcing the government to react to protect its citizens. The first one identified in the prologue, a giant lizard-like creature called Gomess, emerges from a tunnel under construction, prompting the Japan Self-Defense Force to respond, successfully defeating Gomess with their tanks. Next, the appearance of a massive flower, the Mammoth Flower, surfaces near Tokyo Station, spewing pollen everywhere; the JSDF only defeats this lifeform with a combination of carbon-dioxide gas and fire. A third massive monster, the bird-like Peguila, proves more challenging as it subjects Tokyo to an unexpected ice age. It takes the work of a scientistnote to discover Peguila's weakness, leading to its defeat. Eventually, the Japanese government officially gives these lifeforms an official label: Kaiju, also known as "Powerful Calamity Beasts" or "S-Class Species".
After a second flying Kaiju, Larugeus, appears and soon disappears, the Japanese government officially forms the S-Class Species Suppression Protocol enforcement unit, a group of five people tasked with the direction of government resources to eliminate Kaiju threats. The initial team consists of unit head Tatsuhiko Munakata, squad leader Kimio Tamura, strategist Shinji Kaminaga, non-particle physicist Akihisa Taki, and biologist Yumi Funaberi. The newly formed SSSP discover early success after their operations to neutralize the snail-like burrower Kaiju Keigel, and the radioactive-material devourer Kaiju Pagos.
The SSSP head to Yamanashi Prefecture by helicopter, in response to a new Kaiju rampaging through the metropolitan area. Based on their observations on its behavior, the team gathers that this Kaiju can turn itself invisible, and has an appetite for electricity. Eventually, the beast is given a name by the DPA's head: the Invisible Kaiju, Neronga. The SSSP has the power substation temporarily shut down, but this only makes the Kaiju angry, and its recent feast on electricity gives it enough power to destroy the JSDF's SSSP-directed missile barrage. As the SSSP rack their brains for a more-effective solution against Neronga, Kaminaga notifies Tamura that there's still someone in the town: a young boy left behind in the evacuation. Kaminaga immediately declares that he will secure the civilian's safety; Tamura gives him the go-ahead.
As Kaminaga finds the boy and leads him to safety, the JSDF notify Tamura that a large object from beyond the atmosphere is approaching the area, at high speed. This large object, a bright red light, smashes into the surface, the force of the impact blast knocking Neronga away and sending debris everywhere. In the sudden instant, Kaminaga shields the boy from the blast, taking debris to his back. As the SSSP tries to get a handle on the situation, Funaberi reports that the object isn't a meteor that crashed onto Earth—it's a humanoid "silver giant" that has landed.
As everyone watches, an angry Neronga sends half-a-million watts of electricity at the silver giant. The sustained attack does nothing to the giant, flabbergasting Taki that anything could possibly withstand that level of voltage. The giant, for his part, merely stands for a moment before slowly walking toward Neronga, slowly building up energy. Once it runs out of electricity, Neronga starts backing away, reactivating its invisibility. The SSSP realize that Neronga is reacting to a threat: the giant's building energy as he sets his hands into a cross formation. Suddenly, the giant fires a bluish-white stream of light at Neronga, destroying the mountain behind it and nullifying Neronga's invisibility before destroying the beast as well.
As the SSSP and JSDF are thrown for a loop by the giant's tremendous capabilities, the giant seems to look behind him at something before taking flight, disappearing from both radar and the naked eye. Meanwhile, Kaminaga carries the unconscious boy to safety, seemingly uninjured...
Word of the silver giant that defeated Neronga has already become the talk of Tokyo as a new member of the SSSP walks to the unit's headquarters in Kasumigaseki, Chiyoda ward. This new member, Public Security Intelligence Agency analyst Hiroko Asami, has joined the team in order to investigate the giant, whom she has dubbed "Ultraman" in her brief report on the matter. To the end of studying Ultraman and his behavior, Asami is partnered with Kaminaga, who was physically closest to Ultraman during the Neronga incident. Asami's attempts to get information leave her disappointed: Kaminaga only reports that he had been knocked unconscious at the time, and for some reason, he asks about what he's supposed to call his fellow SSSP members, or if her term for him—"buddy"—is her referring to him as a work partner. Simultaneously, no one seems to question why Kaminaga has a large amount of books on philosophy and human behavior, or why he's reading those books while working.
Eventually, when Kaminaga later returns to his desk with a cup of coffee, Asami comments on how inconsiderate he is for not having gotten her a cup of coffee, let alone asking if she wanted one. When Kaminaga points out that as people, they are self-sustaining beings that can act for themselves, Asami counters that he's partaking of the efforts of other people (his coffee and his clothing), asserting that humans are social creatures who survive by coming together. Somehow, this leads Kaminaga to liken humans to a herd, further astounding Asami.
Work gets interrupted when a Kaiju surfaces in Aomori Prefecture, emerging from underground with drill-like appendages, prompting the SSSP to move out. Funaberi, having a bad feeling about this Kaiju, discovers that it is similar to the nuclear-waste-devouring Pagos, and the team realize that it's tunneling its way to a nuclear-waster storage facility. They request the US Army launch a bombing run as it moves, but the attempt does nothing to hinder the Kaiju, now identified as "Gabora". As Gabora approaches the facility, and the SSSP are wracking their brains, Kaminaga decides to act: sneaking out of the command tent, he runs into the nearby forest and pulls out a silver cylindrical device. Activating it causes the silver giant, Ultraman, to appear, now with red patterns across his body. Ultraman flies toward the facility, and the SSSP field team sans Kaminaga follow to record and observe.
At the facility, Ultraman intercepts Gabora, and a fight between the Kaiju and the giant ensues. Ultraman behaves with more human-like fighting as he attempts to pacify Gabora without causing any nuclear waste leaks. Eventually, Gabora opens its drill-like appendages to reveal its head; the SSSP, now in the area, recognize Gabora's similarities to Pagos, with Taki realizing that Gabora is about to fire the same kind of nuclear beam that Pagos used. Ultraman immediately blocks the attack, but when he notices the SSSP nearby, he changes his approach: he exposes himself to Gabora's nuclear beam, absorbing and neutralizing the radiation with his own body, and moves against it to reach Gabora. The SSSP decipher his intent from the readings and behavior: Ultraman is protecting the SSSP. And judging by how his red patterns flicker to green amidst the attack, he is doing it at risk to himself. Eventually, Ultraman defeats Gabora by landing a punch on its exposed head, then carries the Kaiju out of Earth's atmosphere.
After they get back, the SSSP are wordlessly greeted by Kaminaga, who seems satisfied that his colleagues have made it back safely.
