When she awakens from her dangerous solo mission, Yuri finds her surviving friends in Battlefront seem to have found peace. In an impromptu “graduation” ceremony, they all take steps to move on to the next level of existence. But this transition seems most difficult for Otonashi, as it means losing his newly formed bond with Angel.

The Shadow monsters show no signs of stopping as more Battlefront members and NPCs fall victim to their strange, marauding power. Yuri takes a dangerous trip into the darkened Guild. In her search to find out just who—or what—is behind these new events, she discovers even darker secrets about herself.

As Hinata and Otonashi talk with Naoi, something strange happens: his shadow takes an enormous, evil form and engulf him. Weapons are powerless to stop the creature. Making matters worse, the Shadow monsters are multiplying and taking control of the members of Battlefront and the NPCs.

Otonashi decides that the high-strung singer, Yui, needs to be pushed into finding peace and “moving on." To do so, he enlists Angel who shows him her new weapon: the dark and evil-looking Hand Sonic 5. But Yui has other plans—namely to beat the boys of Battlefront in a violent game on the soccer field.

With the Angel clone situation becoming uncontrollable, Naoi proposes that they once again call upon the genius hacker, Christ. Meanwhile, Otonashi begins to remember his past.

With Otonashi's and Angel’s newly formed alliance, dark and powerful clones of Angel have begun attacking the Battlefront with greater aggression. They must return to the trap-rigged Guild once more and risk heartbreaking, violent losses.

Now that Naoi has seemingly joined Battlefront, Yui persuades Otonashi to let his powers of hypnosis help him recover his memories. But Otonashi may not be ready to remember such a tragic, painful past. But there are other issues at hand for the group—such as banding together to capture the mysterious creature from a nearby river known only as the Monster Stream.

When Angel is believed to be breaking scholastic code, Naoi uses this infringement to exert his growing power and places both Angel and Otonashi in a prison within the school. They discover that Naoi is using his power in violently, and Angel and Otonashi must escape or risk heavy casualties.

To strip Angel of her scholastic power, Yui devises a plan for the Battlefront to replace Angel’s test results with bogus ones. She will be shamed, stripped of her title of Student Body President, and be out of their way for good. But they never realize the one who replaces her may be even more sinister than Angel could ever be.

With the lead singer of Gldemo now obliterated, a replacement must be found. The manic, high-strung Yui tries desperately to assume the role. Hinata, meanwhile, seeks to avenge a mistake made long ago on the baseball field by assembling the strongest team possible to defeat the other teams in the school. Otonashi worries the game could strike Hinata out in more ways than one.

With the aid of a new member, the genius hacker, “Christ”, Yuri and the Battlefront decide to break into Angel’s lair and steal secrets from her hard drive. To distract the NPCs, they use the girl group Gldemo. But when the teachers interfere, the lead singer suffers a shocking fate.

Realizing they need more weapons in their battle against Angel, the group descends into the Guild. But once there, they realize that all of the hallways, staircases, and passageways have been rigged with deadly traps. It’s a race against time to see if they can get through the violent maze before Angel catches up with them.

After a mysterious accident, a young high school student wakes up to discover he is caught in some kind of violent afterlife where a strange and avenging Angel is pursuing him. Confused and afraid, he joins a band of gun-toting teens intent on destroying the Angel and taking their destinies into their own hands.