The Ultimate Destruction Program has replicated itself into the vaccine Midgard, causing it to turn on its users.
Summary
Urd wakes up after having a nightmare about Fenrir. She is about to go back to sleep when Skuld tells her that she needs to take responsibility for the giant wolf that's in the sky! Urd then notices that Belldandy has broken her seal (an offense so serious it could lead to license termination) and now wants to get back at Fenrir after realizing her sister had done it for her. However, before she can do anything, Fenrir is seemingly defeated by the vaccine Serpent Midgard and vanishes.
The vaccine, however, doesn't disappear after a while, and instead, the serpent crashes to the ground and turns on its creators, attacking them. Belldandy projects a powerful forcefield to protect everyone. Skuld believes that Midgard was infected by the Ultimate Destruction Program and self-replicated, and the serpent proves her right as it now declares that it is the Lord of Terror.
Now, Midgard produces what it claims is the "final key" to the destruction of the universe: a ring-shaped object called the "Universal Superstring—the subject of the untested "superstring theory", where the smallest objects of reality are comprised of string-like lengths as small as 10-35 cm, the vibrations of which create particles and their unique properties that make up the universe. Midgard now threatens to cut the superstring, thereby ending the known universe. Urd convinces Belldandy to lower the shield and tries attacking Midgard with magic, but she is unaware that she already lost most of her energy and her attacks sputter out. Skuld tries her hand and throws explosives at Midgard.
A miniature Keiichi asks why Midgard is bothering with attacking them when it could just scurry off somewhere and cut the superstring already, and Belldandy believes that it may require something else to actually cut it. While Urd keeps Midgard busy with Skuld's explosives, Belldandy tells Skuld to bring out the vaccine's manual again and they read through it to figure out how to destroy Midgard.
Once they find what they're looking for in the manual, Belldandy takes the vaccine flute in her hands and plays a melody on it compelling Midgard to vanish from the world. A bright light emanates from the flute, and Midgard quickly turns to whatever target it can so it can self-replicate again, choosing Skuld. Before Midgard can reach her, however, Keiichi throws himself into Midgard's mouth, making it recoil because he tastes bad. Midgard has vanished, and firefighters have now arrived to put out the flames that have engulfed the Maruhaku Messe convention center.
Everyone returns to the ruins of the Temple and Keiichi asks Belldandy to return him to normal size. As soon as that happens, however, Keiichi is acting different than he normally does, as if he's another person. Meanwhile, Urd gets one of the TVs working and they find out that the giant superstring above the Maruhaku Messe hasn't disappeared yet, meaning the Ultimate Destruction Program is still active.
Suddenly, Keiichi snatches the Flute of Midgard from Belldandy's hands and transforms himself into a demon, having become the third vessel for the Ultimate Destruction Program. While Urd and Skuld don't take him seriously, Belldandy is distraught at how this could have happened.