Otonashi befriends Kanade and invites her to join in on SSS activities. Otonashi regains his memories with the aid of Naoi's hypnosis and agrees to continue with the SSS.

Naoi uses powers of hypnosis to control NPCs to fight for his own interests against the SSS, but Otonashi stops him after acknowledging Naoi's existence and he subsequently joins the SSS. Angel, whose real name is Kanade Tachibana, loses her position as student council president and the vice president Naoi succeeds her. The first of the characters to fulfill her dream and pass on is Iwasawa, the leader of Girls Dead Monster. The rest of the afterlife school is populated by a large number of 'normal' students and teachers Yuri deems 'non-player characters' (NPCs) as they are not human, but look and act the part. Angel creates her powers with the aid of a computer program called Angel Player.

Their only enemy is Angel, a girl who has supernatural powers and fights against the SSS. In the SSS, there is a four-girl band named Girls Dead Monster that acts as a diversion during missions, and an organization called the Guild that mass-produces weapons out of dirt and supplies them to the SSS. He meets Yuri, a girl who invites him to join the Afterlife Battlefront (死んだ世界戦線 Shinda Sekai Sensen (SSS)?), an organization she founded and leads which fights against God for the cruel fates the SSS members experienced in life. The story follows the main protagonist Otonashi, a boy who lost his memories of his life after dying. Those in the afterlife school can still feel pain as they did when they were alive, as well as dying again, only to awaken later with no injuries. Angel Beats! takes place at a high school acting as a limbo for those who have died, where students learn to give up any lingering attachments they still have from life before passing on.

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