Plot
The story takes place during the third spring since Belldandy's arrival. Celestin, a former mentor of Belldandy, is released by Morgan Le Fay, and erases all memories of Keiichi from Belldandy to use her as a virus to hack the Yggdrasil computer in the heavens.
Morgan heads to the Lunar Prison on the Moon and releases the seal. She is able to make contact with a small mask that reveals that they must unite for their common goal.
On Earth, it is the start of the New Year. The Motor Club i tries to lure new applicants with a display of the vehicles they race with, including the new two-seater Keiichi Morisato and Belldandy will be using in an upcoming race.
That night while the club members celebrate, Keiichi inadvertently finds himself in a compromising situation with a fellow club member. Belldandy runs outside, with Keiichi in pursuit. The two share a moment in a flurry of cherry blossoms before being interrupted by Celestin, a former mentor of Belldandy. Celestin gives her a kiss, whereupon Belldandy collapses infected with a virus. Peorth calls to inform Urd that Yggdrasil has also been compromised by the virus, and must isolate The Heavens from Earth as a security measure. Until the matter is resolved, Belldandy cannot receive treatment.
When she finally regains consciousness, Belldandy can not recall memories of Keiichi, even though she can identify Skuld and Urd immediately. Urd recognizes the symptoms as selective amnesia and informs Keiichi that all of Belldandy's memories after their first encounter must have been sealed. Skuld attempts to restore Belldandy's memory with a number of inventions, but fails. Unable to find an immediate solution, Keiichi decides to accept the current situation for the moment, and try to live as normally as possible.
When the Motor Club is told about Belldandy's condition, they are shocked, but also concerned about their upcoming race; the competition is a mixed-gender race. The newcomer Morgan offers to take Belldandy's place. Unsure about her skill, the club gives her a trial-run with Keiichi; seeing them ride the bike causes some traces of memory to return to Belldandy.
Up to this point, Keiichi has managed to remain stoic despite Belldandy's condition. However, as he drives back to the temple that night at dangerously high speeds, he is so immersed in his troubles that he subconsciously makes a sharp turn unaided, almost causing an accident.
When Belldandy accidentally uncovers a photo album filled with pictures of the two at the temple, she realizes how deeply her amnesia has affected Keiichi. Inspired to know him better, Belldandy opts to remain as Keiichi's partner in the upcoming race despite her amnesia. When an irritated Morgan hears about Belldandy's renewed resolve, she challenges Keiichi and Belldandy to a race, teaming up with Megumi at Keiichi's request. Despite Morgan's best efforts however, they are no match for the two and the experience unlocks more of Belldandy's memories.
That night, Belldandy accidentally overhears a discussion between Keiichi and her sisters regarding Celestin's role in the current crisis. Realizing that Celestin erased her memories and inserted the virus, Belldandy stumbles out into the night, shocked and confused. Taking advantage of the situation, Celestin lures Belldandy away and uses the virus to turn Belldandy against her elder sister in combat. Keiichi and Skuld's arrival causes a massive amount of uncontrollable energy surge from Belldandy, knocking out everyone in the vicinity. Regaining her identity, Belldandy is able to safely dissipate the energy, though she faints in the process. Skuld wakes up to find the locality ravaged in the aftermath of the battlefield. When she spots Celestin calmly stepping down the stairs, she summons Noble Scarlet and angrily knocks Celestin with a thunderbolt into a screen, causing water to flood. Keiichi awakens just in time to notice the oncoming wave, and rushes to cover Belldandy, so that he will take the brunt of the blow for her. Belldandy awakens to find Keiichi comatose on the ground and hysterically tries to revive him.
Back at the temple, Belldandy comes to her senses, but her heart is uneasy and believes that she has only served to bring suffering to Keiichi. Skuld assures her that, regardless of present circumstances, in all of the friends they have made and all the experiences they have been through, Keiichi and Belldandy have weathered all with smiles. Reassured, Belldandy falls into Skuld's lap, exhausted from the battle.
When Keiichi walks into the empty Motor Club clubhouse alone the next morning, he finds Morgan bleeding on the stairway from the battle. Keiichi insists that she come with him to the hospital wing. While he treats the wound on her arm, Morgan forcibly kisses him; unbeknownst to them, Belldandy sees them through the door. An upset Belldandy prepares herself to accept the vaccine, which will destroy the virus in her, at the risk of erasing all her memories. In coordination with Heaven, the ceremony of administering the vaccine commences, but something goes wrong.
The virus inside Belldandy has been using her as a Trojan horse; since Goddesses are connected to Yggdrasil, it was able to infect the main system through her, although without direct access it was only able to make slow progress. The Heavens made direct access with Belldandy to administer the vaccine, unwittingly allowing it even deeper into the system. More seriously, while usurping this direct link, the virus rewrites itself using the vaccine, turning itself into a program that bypasses all of Yggdrasil's security measures. Exploiting the direct link between Belldandy and Yggdrasill, Celestin hacks deep into the system mainframe, accessing an enigmatic program referred to only as top-secret. He possesses Keiichi and pulls the program through Belldandy, incorporating it into the vaccine mandala. This creates an enormous magical field that swallows the temple and the surrounding forest. Three enormous tree trunks spiral from the ground into the sky, and a gargantuan being slowly materialized.
A flashback shows Celestin concerned with the Gods' ambivalence to the lower worlds' suffering. Celestin tried to rise up against them, first by destroying the Gate of Judgment. Heaven's agents are sent against him, but Belldandy manages to stop them temporarily before more agents are sent and both are restrained. Celestin was then sentenced to eternity in the Lunar Prison, while Belldandy's memories of the events were erased by Urd.
Flash forward to the present, if Celestin destroys Yggdrasil and the entire Earth, a new Earth free of suffering will have to be created. The three Goddesses stand united against Celestin and Morgan, trying to stop them. Back in the Heavens, Peorth authorizes the use of Gungnir to stop Celestin. She launches the attack, but Belldandy manages to protect him at the last minute: they may be attacking Celestin, but it is Keiichi that would be killed. Keiichi then helps Belldandy block the attack by borrowing Celestin's power (with his permission). Realizing he was wrong, Celestin finally concedes, and releases Keiichi from his body.
Soon after, Belldandy, Keiichi and Morgan are transported to the Gate of Judgement. Having once lost her love when trying to pass this test of the Gods, Morgan warns the two to not pass through it, but they move forward, with complete confidence they will pass through safely and not be separated. Upon stepping through the gate, they return to Earth. As they return, Morgan tells them that she will stay and tell future couples the story of how they passed the test. The two return, but back in the Heavens, Yggdrasil is critically damaged. The three goddesses and their angels come together to sing and rapidly restore The World Tree, before dematerializing it. Finally by herself, Belldandy informs Keiichi that the virus deleted Yggdrasil's records, meaning that he is once again free to ask for any wish. Smiling softly, he replies, "That's easy," sparking their love for one another once more.
