It's been 15 years since the outbreak of Ultra Flares on the sun that cause the Spark Dolls around Earth to turn into monsters. Officer Oozora Daichi, a member of the defense unit created to deal with these creatures, is confronted with a rampaging Demaaga, who can scorch anything with it's intense flame. Daichi then hears a mysterious voice from his multi-device.

The Giant Bird Monster, Birdon appears in Ookumayama. And it looks like it's getting ready to spawn. But when civilians are discovered trapped within the nest it builds in order to lay it's egg, Daichi and the Xio team begin a rescue operation. Attacking Birdon to lure it away from the nest, the creature becomes enraged. Daichi unites with Ultraman X to save his friends.

Daichi and Asuna are sent to investigate a string of localized earthquakes. Daichi spots a suspicious woman once they arrive. Not only that, but she then calls forth the monster, Teresdon, from underground. After driving the creature away with flares, the duo are then ordered to look into the identity of the woman. Someone matching her appearance is discovered, but that person is already dead.

A Zarab alien sends Bemstar to Earth in order to destroy it! Daichi is missing after getting caught in the beast's rampage, causing Asuna to lose control. After her failed attack, Ultraman X is absorbed into Bemstar! At the same time Wataru and Hayato pursue the Zarab alien, their rivalry prevents them from being able to complete their task of defeating the alien.

Experiments are underway to find the means for Xio officers to turn monsters into Spark Dolls. The monster Black King strikes, with Daichi and X uniting to fight it, but the Alien Nackle uses this opportunity to steal the Spark Dolls from Asuna.

A young man named tE rU is causing a commotion in the city. Is he an alien? When he goes inside the mechanical giant Rudian it begins to march on the city. But after seeing tE rU heal an injured girl, Daichi unites with Ultraman X and attempts to stop Rudian, believing that it's not acting maliciously. With tE rU in custody, Xio examines Rudian, and a shocking fact comes to light.