|A solar flare called the Ultra Flare (ウルトラフレア Urutora Furea) has awakened mysterious OOPArts known as Spark Dolls from the depths of the earth and the ocean, materializing them into rampaging monsters that terrorize the Earth. Due to this, UNVER was formed to gather, collect and secure unstable Spark Dolls and a new attack team was formed, Xio to combat monster threats.|
Fifteen years later, Daichi Ozora, a member of Xio's Lab Team whom was orphaned when his parents lost in the Ultra Flare, bonds and transforms into Ultraman X to battle threats from both aliens and monsters. He soon learns of the truth behind Ultra Flare and resolves to help Ultraman X to regain his physical body after the incident had trapped him in a form of computer data.
In the middle of the series, Daichi learns of how to properly summon a Cyber Monster and thus, bringing forth Cyber Gomora, a monster modelled after his childhood Spark Doll, Gomora, becoming one of Xio's new ally and alternative for Daichi whenever X is unable to fight. At the strange time, a strange energy source dubbed by Xio as Dark Thunder Energy (ダークサンダーエナジー Dāku Sandā Enajī) frequently appears and turns ordinary monsters into berserks. Because of the energy's effect also weakens X, it nearly killed him during his fight with Tsurugi Demaaga, the first victim of Dark Thunder Energy. To counter this, a new weapon was discovered by Daichi, the X-Lugger, which allows X to become Ultraman Exceed X and use the weapon to purify monsters from Dark Thunder Energy. In accordance to an alien named Dada, humanity is on the verge of extinction from the effect of Dark Thunder Energy's assault.