The space station includes a function that works in conjunction with the Rider System's Clock Up function. By building the Jacob's Ladder space station, they plan to capture this meteor and spread its water throughout Earth, replenishing the Earth’s oceans. At the same time, ZECT has obtained intelligence about a large comet orbiting the vicinity of space.

With three groups in existence (Neo-ZECT, ZECT and the Worms), Soji Tendo has decided to sell his power to either Neo-ZECT or ZECT, but his intentions are unclear. Daisuke Kazama and Shura Hokuto are also part of Neo-ZECT. By present time, power struggles in ZECT have caused a new group, known as Neo-ZECT, to be created by Hidenori Oda. The battles lasts over seven years, depleting Earth's resources and turning it into a barren wasteland. In order to counter this new threat, ZECT was formed, who in turn created the Masked Rider System to combat the Worms. These creatures took on the identities of real humans and then killed them.

In 1999, an enormous meteor crashed onto Earth carrying extraterrestrial creatures known as Worm within it. However many elements in this film do not match with aspects that are revealed later in the main universe, primarily regarding Hiyori Kusakabe, her relation to Soji Tendo and what really happened not just on the day of the meteor strike but some time before the meteor due to a different nature to the Worms on Earth in the main universe. This film itself is an alternate-universe of the main Kabuto universe however its impact does appear to affect the main universe in its climax, where the meteor sent to strike Earth in this world instead is sent seven years in the past and leads to it becoming the meteor that destroys Shibuya in the prologue of the main universe therefore, this film, despite having elements that include the first appearance of Hyper Kabuto, technically occurs prior to the series with the explanation of the Shibuya meteor.

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