A meteor shower deposits a large object in northern Japan. When the military investigates, they find an empty crater. A series of strange events marks a trail from the impact site south to the city of Sapporo, culminating in an attack on a commuter train. The culprits are large, insect-like creatures that allegedly came from space in the meteor shower. They plant a large flower, which gives off immense quantities of oxygen. Honami, an astronomer, realizes that the creatures intend to spread and multiply by launching a “seed” into space. However, the blast from the launch will obliterate Sapporo. Gamera appears and destroys the flower before it can launch a seed. He is overwhelmed by the smaller creatures, and is forced to flee. A giant alien insect bursts from the ground and flies away. The air force shoots it down, but cannot retrieve the body.

Honami meets with Watarase, who has been investigating the case for the military, and pool their knowledge. The creatures, now known as “Legion,” are made of silicon and communicate through electromagnetic waves. Everyday electronic devices interfere with their communications, so the Legion see mankind as an enemy, and big cities as their “nests.” The Legion purposely planted their flower in Sapporo to destroy it and take over, like an invasive species. Since Gamera prevented the launch, the military is on high alert waiting for Legion to reappear and try again. Sure enough, a large flower blooms in Sendai. Gamera returns, and faces off against the Giant Legion. The Giant Legion buys time for the flower to complete its growth, but Gamera barely manages to divert it before the blast incinerates Sendai. Gamera is presumed dead from the explosion, leaving the Japanese to face the final assault without his help. Fortunately, Honami and Watarase learn that a particular electromagnetic frequency attracts the smaller Legion, and they plan to exploit it to draw them away from the battle if things get to dicey. Defense lines are setup all along the Legions presumed final target: Tokyo.

The Giant Legion leads the attack, breaking through the first defense line while sending the smaller Legion to scatter the air force. A small gathering of despondent children gathers in the ruins of Sendai to hold a vigil for Gamera. Gamera draws strength from them and revives. He immediately takes off for Tokyo. A nearby power plant is used to distract the smaller Legion so Gamera can concentrate on the Giant Legion. Just as Giant Legion is about to break through the final line of defense and enter Tokyo, Gamera summons a powerful energy attack that completely obliterates his foe, saving the city.