This movie takes place in an alternate universe (where its storyline could be considered a prequel to the events of the TV series). In 1999, an enormous meteor crashed onto Earth carrying extra-terrestrial creatures. In order to counter this new threat, ZECT was formed. Seven years later, in the year 2006, power struggles in ZECT have caused a new group, known as Neo-ZECT. With three groups in existence (Neo-ZECT, ZECT and the Worms), Tendou has decided to sell his power to either Neo-ZECT or ZECT, but his intentions are unclear. ZECT reveal a plan to save humanity, but unknown to other is a plot to destroy man kind.

Arata Kagami seeks to get the Hyper Zecter just like Soji Tendo, so he tries to emulate Soji. Once he realizes that he has to be himself, the Hyper Zecter appears and allows him to transform into Kamen Rider Gatack Hyper Form.