Professor Nakatani, aided by SSSP member Arashi (acting as his guard), goes on a scientific expedition to the Johnson Islands. They discover that the legendary kaiju Gomora is still alive, and Nakatani decides to bring the still-living kaiju to a museum for the World's Fair. The SSSP agrees to do this task, despite the utter illogic and danger of bringing a living kaiju to a largely populated city. Before the kaiju attacks them, Arashi tranquilizes the kaiju with the UNG Dart, and the Patrol airlifts the kaiju via nets with the Jet VTOL. However, the kaiju awakes an hour early due to atmospheric changes between the island and the mainland and struggles to the point where the VTOL's have to release the nets, thus causing the kaiju to fall two kilometers to the ground. Enraged, Gomora goes on a rampage on Mount Rokkô (where he landed), and Ultraman, who comes to the rescue, is unable to stop the kaiju, and is beaten, much to everyone's shock. Even worse, somehow in the fight, the Beta Capsule is knocked free from wherever its stored in Ultraman and its retrieved by a kid nicknamed the Monster Prince due to his fascination with kaiju.
When Gomora continues his rampage, Hayata of the SSSP uses the powerful Mars 133 gun, invented by Ito (Ide) to counter the second appearance of the Baltans, and succeeds in severing his tail. But the kaiju burrows under the ground in retreat, and later appears at Osaka Castle. The Patrol is ordered to save the castle at any cost, however Gomora smashes the castle. As the kaiju pursues Ide and Arashi, the child returns the Beta Capsule to Hayata. Hayata tells the kid to run and hide then uses the Beta Capsule to transform back into Ultraman. Ultraman saves the day by breaking the Kaiju's nasal horn and left crest and blasting him in the forehead with the Specium Ray. Hayata rewards the Monster Prince by giving him his communicator-insignia and tells him to study hard and not obsess over kaiju.