SPOILER WARNING: This section may contain major plot and/or ending details. Proceed at your own discretion.
In a ruined Las Vegas, Steven Woods contacts Professor Allison and learns about the Jet Jaguar Project, led by Yumi Nagata, and Jet Jaguar himself, who is staring down Godzilla. Godzilla fires an atomic blast at Jet Jaguar, believing he was his enemy, but Jet Jaguar dodges it and turns Godzilla's attention to Gigan. Now a team, Jet Jaguar and Godzilla fight Gigan together until Jet Jaguar notices Orga is regenerating and tries to pulverize his remains. Gigan and Godzilla continue fighting as the Star Falcon shoots at Gigan, the Land Moguera team standing by. Woods talks with the crew of the Star Falcon and decides that he and Chavez will look at what Jet Jaguar is doing nearby. When they get there, they see Orga regenerating. The Millennian UFO shoots Jet Jaguar, knocking him down, and proceeds to retrieve Orga's organic material, along with Steven Woods and Chavez, and flies away. The UFO catches Godzilla's attention, letting Gigan stab Godzilla's foot with his scythe, which Godzilla counters by firing his atomic breath at him twice, forcing Gigan to retreat. Then, Jet Jaguar shows up, but Godzilla fires his atomic breath at him and also slams his tail against him. Jet Jaguar then punches Godzilla in the face and drops him out at sea later on. Las Vegas is secured, and Yumi describes how she learned of Jet Jaguar, and talks about Allison about the possible threat he is, which she assures he isn't.
Meanwhile, in the Cryogs' spaceship, the Cryog leader is talking with a Devonian about conquering the Earth, the Devonian reminding the leader that they'll take half the planet. After the transmission cuts, the leader reveals that he wants the planet for his race only. Another Cryog comes in and shows the leader to the Millennian UFO, saying Orga and something else are in it. A hole opens up under Woods' and Chavez's feet, making them fall right in front of the Cryog leader, who begins taunting and choking them. Just then, however, Jet Jaguar shows up and punches a hole in the ship.