On what seems to be a normal day for the Earth, a massive invasion fleet of alien ships mass near the moon. The SSSP's Paris base radios in at the SSSP base in Japan that the coming fleet may very well be the largest invasion fleet ever deployed against the Earth.

Taking matters into their own hands, the SSSP, sans Fuji and the visiting Dr. Iwamoto, take to the skies in their VTOLs and easily wipe out many of them. Unfortunately, back at the base, Iwamoto attacks Fuji and proceeds to destroy the base's supercomputer. Soon, Hayata, Captain Muramatsu, Ide, and Arashi return to find the base in chaos. Ide assists Fuji while his comrades chase down Iwamoto. Arashi catches up with the latter, and punches him, revealing the face of an Alien Zetton, who'd incapacitated the real Iwamoto beforehand. Hayata quickly shoots the alien, who simply says 'Zetton' before evaporating. Suddenly, a final alien ship, much bigger than the ones that had been destroyed earlier appears and unleashes a monster called Zetton.

While Arashi runs back to the base to rescue Fuji and the real Iwamoto, Hayata transforms into Ultraman and soon, the silver giant and Zetton clash. In the ensuing battle, Zetton damages Ultraman's Color Timer, leaving him unable to fight. But Ide and Arashi then shoot Zetton with Dr. Iwamoto's creation, a special anti-gravity missile that kills the monster.

Soon after, Zoffy, an Ultra Warrior of higher rank than Ultraman, arrives in a Travel Sphere to revive his comrade. The two engage in conversation. (In the Japanese original, Zoffy debates with Ultraman about Hayata. In the English version, Zoffy, who is not mentioned by name in this version, inquires about why his subordinate has lost to Zetton, and is told about Zetton's use of the unexpected weapon that damages Ultraman's warning light.) Ultraman requests that Zoffy split his and Hayata's life forces that Hayata may live a normal life, and also that he may regain his own powers and return to Earth. Zoffy complies with both requests, and Hayata ends up where Ultraman had fallen. The SSSP wave Ultraman goodbye, and a clearly amnesiac Hayata is left with the Beta Capsule. (In the English version, Hayata keeps his memory and joins his friends in seeing Ultraman and Zoffy off.)

As the narrator promises that Ultraman will return to the Earth someday, the last shot of the series is Zoffy and Ultraman flying home together back to Nebula M78.

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