During the Ancient times, a Kaiju named Zaigorg rampaged on Earth until a group of Ultra Warriors (among them was Ultraman Tiga) appeared and sealed him in a temple on Earth, using a blue stone as a lock to their seal. Before leaving, Tiga left his stone statue and a petrified Spark Lens for future generation to use.
Sometime ago, Ultraman X fought against an unknown purplish figure in his Flash Travel mode. X emerged victorious, when he knocked his opponent to the sun but this became his undoing, which initiated a solar flare that bathed the Earth in a purple light and awakened Spark Dolls from beneath the Earth. As a result from the battle, X's body was digitized and sent to Earth.
During his time on space, he received a strange frequency that originated from Daichi Ozora, his future human host.
Fifteen years later, when the monster Demaaga rampaged on a city, he rescued and bonded with the Xio officer Daichi Ozora, where his body was finally re-materialized. X and Daichi where able to confront and destroy Demaaga.
At the end of the series, the mastermind behind the Ultra Flare and Dark Thunder Energy appeared, namely Greeza. Having destroyed three planets in the past, it was thought to be killed after X banished it to the sun but instead survived and had journeyed through Mercury and Venus within 18 days. Now arrived on Earth, Greeza sought to absorb the Spark Dolls to achieve its strongest evolution and X revealed himself to Xio members, seeking cooperation to defend their supply of Spark Dolls from Greeza. In the end, X and Daichi seemingly died after performing a kamikaze attack but Greeza survived its destruction and successfully absorbs Xio's Spark Dolls, finally achieving its final evolution. It wasn't until Asuna managed to bring Daichi back to the real world and X revived, with both managed to pursue the captured Spark Dolls to escape and merged with the Ultra to finish Greeza. Although the destroyer is killed, X however is yet to regain his true body, while continuing his service in Xio.
Ultraman X The Movie took place after the end of the series.