In present times, Gods and Demons coexist together with Humans after the door between each of these worlds had opened. Tsuchimi Rin is a normal young high school student attending Verbena Academy, spending his days living peacefully with his childhood friend Kaede. Unexpectedly, one day the King of Gods, the King of Demons and their families move into be Rin's next door neighbors. Apparently the daughter of the Gods, Sia, and the daughter of the demons, Nerine, are both deeply in love with Rin after having met him in the past. Along with his playful friendship with upperclassmen Asa and his encounter with the silent but cute Primula, Rin has much on his hands dealing with the affections of each of these girls. Based on the eroge by Navel.

Strange suicides have been taking place in New York. One day, four girls from the same high school wake up in the morning feeling tired and dizzy and not being able to remember anything about the previous night. In school, they find out that one of their classmates has committed suicide. School is canceled for the rest of the day, but instead of going home, the girls are drawn to a park by butterflies only they can see. Suddenly a man and a woman approach the girls, telling them that they all died the previous night. (Source: ANN)

A runaway vehicle driven by Izumi Yasaka, en route to the Public Safety Bureau building, is reported shortly before it crashes into the building. Izumi is a counselor who recently ran away while working at a latent criminal isolation and rehabilitation facility known as Sanctuary. Before Inspectors Mika Shimotsuki and Akane Tsunemori get to interrogate the suspect, a sudden request is issued from the facility to promptly bring Izumi back. Interpreted as a direct order from the Chief and the board at Sanctuary, the Inspectors obey, but insist that Izumi be escorted back personally. Tsunemori intends to investigate further with the rest of the team at the Bureau. Now Inspector Shimotsuki has finally been given the opportunity she had been waiting for—to be the primary investigator on an important case. This case follows Shimotsuki and her team of Enforcers as they uncover the secrets of Sanctuary.

Mii Snowdon is left on her own after her father disappears while investigating the mysterious letter-shaped pokemon called the Unown. The only clue to her father's disappearance is a box containing several tiles. While playing with these tiles, Mii makes a wish to see her father again, and this wish awakens the Unown—who summon the lion-like, legendary pokemon Entei to act as her father.

Meanwhile, Satoshi heads to Greenfield with his faithful pokemon companion, Pikachu, to meet with his friends, Kasumi and Takeshi. When they reach the area, they are shocked to find the place crystallized. They quickly learn that the Unown are responsible for this, and that they will need to be defeated in order to restore Greenfield to its former beauty.

The situation becomes personal when Satoshi's mother is kidnapped by Entei. To discover why his mother was taken away, Satoshi, along with his friends and pokemon, must travel the crystallized landscape to confront Entei and the Unown. 

[Written by MAL Rewrite]