The story opens as a young fairy unlocks a strange device located on Earth's moon, freeing a small face-like icon, with markings resembling that of the goddesses...
It has been three years since Belldandy and her sisters arrived on Earth, and things have been going relatively smoothly. Belldandy has become Keiichi's riding partner in the Motor Club, which is preparing for a big sidecar motorcycle race.
Celestine, Belldandy's former mentor, suddenly arrives after mysteriously vanishing years ago. He is jealous of Keiichi and believes that Belldandy should be his. To prove his point he removes all of Belldandy's memory from the last 3 years. She no longer remembers Keiichi at all.
Meanwhile a malicious computer virus is attacking Heaven, if it is not stopped it may destroy the entire system, and the worlds they govern along with it. Keiichi and Belldandy's sisters try to revive her memory, Peorth is busy attempting to stop the destruction of Heaven. Peorth heads up to see the powers that be and she is given a solution. The answer may come from exploring Belldandy's past, a journey that will unlock many hidden secrets, and put the powers and personalities of the goddesses to their most critical tests.
Meanwhile back in the Motor Club a new girl has arrived who can match Belldandy in everything, even her love of Keiichi.