On one rainy day, an Adapter attacks the passengers on a tram. Luckily, Aoto, another Adapter who was at the scene, stops him with his ability. Akane and Midori are ordered by the Academy to recruit Aoto, but they hear a disturbing rumor about him.

For Akane, his father meant the world, so he cannot understand why Aoto would kill his own parents. However, Aoto does not share his story either. The colliding two run into each other later, when a patrol Driver suddenly starts to malfunction.

The memory of her and her friend is the reason why Midori pursues the Divine Gate. When Arthur announced that they will start the search of the Divine Gate, Midori has mixed feelings; She wants to find the answer to her question, but she is also afraid.

Concerned about Aoto's emotional disconnect, Akane and Midori look him up on the academy server, but his information were classified. Determined, the two steal Undine's access pass and finds out that Aoto is a suspect of the Blue Christmas massacre.

Akane and the team go to an abandoned section for special training. During the latter part of their training, they meet a group called "The Defiers." Hybrid of human and animals, they have super strengths, and begins attacking Akane and the team.

Lead by Arthur, the Knights of Round and the Adapters from the Academy head for the Divine Gate. Arthur explains that his wish is to destroy the Gate and return the world to its original state. However, Loki and Oz stand in their way to stop them.

Akane and the team were able to escape the collapsing Divine Gate, but Arthur has gone missing and the World Council has imposed a martial law to find everyone. Meanwhile, Loki joins the Geniuses of Divine and has something else up his sleeve.

Akane, Midori, and Aoto are separated from their advisers and magically find themselves acting in a play, conspired by Loki and Shakespeare. As they are forced to play their part, they each meet someone who they've been looking for...

After escaping Shakespeare's divine play, Akane, Midori, and Aoto find themselves inside the zone. Aoto already holds the key to the Gate, but Akane and Midori do not. Unfortunately, Loki already has that figured out, and great tragedy awaits the two.

With "despair" being the key to the Divine Gate, both Akane and Midori's loss of their significant person tragically gives them access to the Gate as well. However, Aoto is up for more despair as he faces his twin brother, Ariton.

Led by the spirit of the key, Akane, Midori, and Aoto reaches the front of the Gate. There, the Key gives them the option to choose their own fate. However, they quickly learn that the Divine Gate is much more than just something that grants wishes...