Fifteen years after the incident, Xio officer Daichi Ozora was studying the Cyber Cards until the emergence of Demaaga attacking nearby citizens. At that time, an unknown voice was heard by Daichi, which came to Earth and fused with him, giving birth to the new warrior, Ultraman X.

Huge Giant Bird Birdon has emerged from the Mt. Okuma. Birdon set up a nest for its eggs but in the process traps several civilian captives in the pile. Angered by the attack as Xio tries to save the trapped people, Birdon rampages and Daichi as Ultraman X arrives on the scene but both soon succumb to the poison injected by the monster. At that time, Alien Fanton Guruman triggers a secret operation!?

Daichi and Asuna were sent on surveying a suburban area after a series of earthquakes reported. While patrolling, Daichi came across a mysterious woman. In addition, she appears every time the underground monster Telesdon emerges. While Telesdon retreated after being attacked with flares, Daichi and Asuna are task to discover the mysterious woman's identity. Said woman resembles an unknown civilian in real life, whom died sometime prior.

Alien Zarab had planned for destruction by making Bemstar attack the city. Asuna thinks that Daichi had got caught up in this attack and has died. Her panicked attack had also caused Ultraman X to be stuck inside Bemstar's body. Also, Wataru and Hayato were following Zarab but because of their rivalry they lost him. Captain Shotaro had told them that Team Work is important. Asuna and other Xio Members decided to unite and rescue Ultraman X.

While Xio members perform experiments to turn monsters into Spark Dolls, Alien Nackle appears and attacks the test site with Black King, while he takes the opportunity to steal the Spark Dolls. As he disappears into another dimension with the van, Rui unfortunately is stuck in the van, and contacts the team.To save Rui, X & Zero join forces.

A man named tE-rU appears in the city & makes trouble to others. Is he an alien? He came to earth by controlling & riding an Mecha Monster called Rudian. tE-rU heals an girl who was injured. By seeing this Daichi Oozora realizes that this person has no evil intention. He Unites with Ultraman X to stop the movement of Rudian. Xio were protecting tE-rU & Rudian & when Xio were knowing about those two, they learn a fearful truth. A Monster named Gargorgon was aiming at Rudian & he will land on earth very soon.

Magical Beast Gargorgon was aiming at the Energy of Planet Gold which was hidden inside Rudian. During the fight of Ultraman X with Gargorgon, X was turned into a statue. Prince tE-rU is deeply regretting that because of the bullet that was aimed at him by Gargorgon, Ultraman X got defeated. Gargorgon tells humanity to surrender & send tE-rU to him. Now it's up to Xio to defeat Gargorgon, revive X & save humanity from the crisis.

When a plant-like monster appears in a small village, Xio tries to heal its apparent malnutrition. But is the Monster as sick as their think it is?

When Gomora finally materializes from Xio's Cyber Monster experiments, but refuses to listen, Daichi becomes obsessed with figuring out why.

Freed by Daichi and Xio, and joined by Hikaru Raido who had defeated the Spectre forces in the UPG world, Shou teaches Daichi some sword techniques to fight better. But will it be enough to stop the combined Guar army and the Spectre siblings in a combined form?

Captain Kamiki attends his daughter's wedding but at the same time, Gomess appeared and worse, the monster was charged with the Dark Thunder Energy.

A TV show was held where reporters would record Xio's daily routine for 24 hours. At the same an alien criminal network surfaces and plots multiple kidnappings.

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Space Cat Mu has come to earth, fleeing from mysterious energy strikes. Red King is coming, and is Wataru in love?

A test to materialize Gomora's Spark Doll begins. As everyone is excited about the successful experiment, a Dark Thunder Energy strike turns Gomora into EX Gomora! Daichi unites with X, and is forced to fire their Xanadium Beam. He then hears a voice asking "Is that your idea of co-existence?" The artificial life form M1 confronts Xio!

People are being attacked late at night by Space Beasts. In order to deal with the packs of roving rampaging creatures, Lieutenant Tachibana personally leads a special team into the field. But at the same time the monster Bemular appears in Canada, threatening Lt. Tachibana's children. With all hope seemingly lost, the mysterious silver giant, Ultraman Nexus appears.

The threat that X had to throw into the sun, the cause of the Ultra Flares, Greeza, has finally appeared on Earth. Daichi and X discover Greeza is headed towards Xio HQ Japan in order to absorb the life energy of the Spark Dolls, and they unite in front of Asuna to stop him!

X and Daichi are missing after being defeated by Greeza... Asuna senses Daichi is alive inside of X's Color Timer, and enters digital space in order to retrieve the duo. Can Asuna's voice reach them? Facing Greeza, who has absorbed the Spark Dolls and evolved into his ultimate form, is there any ray of hope to be found?

Daichi and the rest of Xio meet the esteemed Dr. Touma Kaito, even as Zetton rampages through the city. Dr. Kaito and Xio work on a way to stop the kaiju, but it is revealed he is an imposter, as X is overtaken by a form of a virus and forced to fight alongside Zetton. However, as the real Touma Kaito appears and turns into Ultraman Max, X is forced to fight him.

Wataru's younger brother, Isamu, once dreamed of making it big as a rugby player. But he somehow ended up living in a sharehouse with a bunch of aliens!

An unknown female alien summons another Demaaga to fight X, and times the fight to coincide with a burst of Dark Thunder energy, which strengthens Demaaga into Tsurugi Demaaga, but weakens X to the point that X disappears, after forcing Daichi out of the fusion. Daichi must resort to a dangerous method to save X, and in the process, remembers a moment of his past with his parents, resulting in an upgraded form for X.

Gina Spectre is able to open up wormholes into other worlds, and through one brings a captured Shou and unknowingly UPG member Arisa (from Ultraman Ginga S). It's up to Daichi and the others to find Shou and stop Gina Spectre as she uses the Dark Thunder energy to her advantage.