During the third spring after Belldandy's arrival, a crisis erupts when Celestin, Hiroshi Yanaka — once a mentor to Belldandy — is freed by Morgan le Fay Ayako Kawasumi and uses a virus to erase Keiichi's memories from Belldandy, infecting her to hack the heavens’ Yggdrasil system. The rescue is complicated by a mysterious message received by Morgan after she frees a seal at the Lunar Prison on the Moon, hinting at a shared purpose that draws the two together.
On Earth, the New Year opens with the Motor Club preparing for an upcoming mixed-gender race and revealing a new two-seater designed for Keiichi Morisato and Belldandy. That night, a near‑misstep with a club member nearly jeopardizes everything, but a moment between Keiichi and Belldandy is interrupted when Celestin again acts, kissing Belldandy and injecting the virus that cripples her ability to trust her own memories. Peorth Rei Sakuma warns Urd Yumi Touma that Yggdrasil is compromised, prompting the Heavens to isolate themselves from Earth and cut Belldandy off from treatment.
When Belldandy awakens, she discovers she has selective amnesia: she cannot recall Keiichi, though she recognizes her sisters, Skuld Aya Hisakawa and Urd. Skuld’s inventive gadgets fail to restore the memories, and Keiichi resolves to live a normal life beside Belldandy as best as he can. Meanwhile, the Motor Club, worried about the upcoming race, agrees to Morgan's proposal to replace Belldandy for the moment. After a test drive with Keiichi, Belldandy’s memories return in faint fragments, and Keiichi, overwhelmed, drives with more speed than control.
Belldandy finds a photo album filled with their shared memories and chooses to remain Keiichi’s partner for the race. Morgan, briefly irritated, challenges them to race against Megumi Morisato Yuriko Fuchizaki and her squad, and when Keiichi and Belldandy win, more memories surface. Belldandy overhears a conversation that reveals Celestin’s manipulation, and she is drawn away by him, who exploits the virus to turn her against her elder sisters in battle. Keiichi and Skuld arrive just in time as Belldandy unleashes a surge of energy that devastates the surroundings. Skuld summons Noble Scarlet to confront Celestin, who is finally struck down but triggers a flood that sweeps through the area. Keiichi covers Belldandy from the rising waters, but the effort leaves him in a coma and Belldandy desperate to revive him.
Back at the temple, Belldandy is shaken by the damage she caused, and Skuld consoles her, reminding her of the strength of their friendship. Meanwhile, Keiichi finds Morgan injured and insists on taking her to the hospital. Morgan, in a moment of tension, forcibly kisses Keiichi, witnessed by Belldandy, deepening the emotional stakes.
As Belldandy prepares to take a vaccine that would erase her memories to root out the virus, the virus—exploiting Belldandy’s link to Yggdrasil—rewrites itself to slip past security. Celestin uses Belldandy as a conduit to hack into Yggdrasil’s core, pulling a top‑secret program into the vaccine’s magical mandala and creating a massive field that materializes colossal tree trunks and a giant being.
A flashback reveals Celestin’s rebellion against the Gods due to their indifference to mortal suffering. After his attempt to destroy the Gate of Judgment, he was imprisoned in the Lunar Prison, and Belldandy’s memories of the event were erased.
In the present, the Gods unite to stop Celestin and Morgan from destroying Yggdrasil and Earth, an act that would require birthing a new world freed from suffering. Peorth authorizes using the spear Gungnir, but Belldandy shields Celestin from the attack to protect Keiichi. Keiichi borrows Celestin’s power to aid Belldandy in blocking the strike, persuading Celestin to relent and release Keiichi from possession.
The trio is transported to the Gate of Judgment. Morgan warns them not to pass, having once lost love on such a test, but they press forward and return safely to Earth. Morgan stays behind to tell future couples their story.
Back in the Heavens, Yggdrasil is critically damaged, and the Goddesses and their angels sing to restore the World Tree before dematerializing it. Alone, Belldandy tells Keiichi that the virus erased Yggdrasil’s records, freeing him to make any wish once more. Keiichi smiles and replies, > “That’s easy,” rekindling their love.
