The angels' roles are to assess the progress of humans giving them positive and negative scores based on their everyday actions.

Despite an incident in Hong Kong where Chihaya exposed his wings to someone, both he and his partner are given a new assignment to study human activity in Shinjuku.

The woman who is named Takako is actually a gynoid, created for the purpose of further study by Dr. Ashino, so that he can try and ascend humanity to the level to God.

Takako escaped from a facility called The House where they were about to implant a fail safe system into her which would reduce her experience to human emotions and therefore not bring her blood to a boiling point, where her heart could self-destruct and take out a large area of the city and killing many people.

Soon both she and Kagetsuya go to The House to rescue Chihaya, of whom Dr. Ashino has taken an interest in that would help him to set the stage for events that take place in the later OVA's.

As Kagetsuya tries to console his partner over breakfast, Aya and Miyagi show up on vacation, and decide to stay in France for a short while.

Chihaya and Kagetsuya's mission is to locate the exiled angel named Sapphire, who has been hiding on Earth ever since his wings became black with cancer.

The partners struggle to help Sapphire while keeping everything a secret from their guests, but Chihaya's exceedingly strange behavior has not been lost on Aya, and she begins to make some deductions of her own.

Both she and Miyagi are well aware of the fact that Sapphire's disappearance has not been taken lightly back in Eden, and as it is, any fallen angels are considered to be a huge disgrace.

His fears are eating away at his heart, and he worries that what happened to Sapphire might be the same thing that caused the abnormal color in his wings and hair.

Picking up where the 1st OVA left off, Chihaya and Kagetsuya are trying to infiltrate Dr. Ashino's lab in order to rescue two black angel children who are being held for interrogation by the mad doctor.

The pair split up to search for the hostages, and while wandering through the corridors, Chihaya discovers, locked away in a side room, a black-winged angel like himself, attached to wires extending from the walls.

The angel's name is Messiah, and Chihaya, desperate to get the dormant figure's attention, exposes his wings at the window of the room.

One morning, while watching the news, Chihaya discovers that Doctor Ashino has arrived in the city accompanied by a strange man in a trenchcoat.

There is no mention of the manga forbidding of homosexuality in Eden, and as such some degree of depth of conflict is missing for characters who show signs of interest in those of the same gender.