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Summer break is now over; the second semester has started for Tomoya, Nagisa and the others, and little has changed. Since Tomoya's relationship with his father is still troubled, he continues to live with Nagisa and her family, even if it means getting roped into organizing a baseball team for the family bakery. Life at school continues as normal with Sunohara as carefree as ever; however, when his sister Mei voices her concerns about him, the series of events that follow place a strain on Sunohara and Tomoya’s friendship. Whether it's saving a person from themselves or passing on a message from the past, one thing’s for sure: no matter how tough things get, good friends will always be there to help out.
The traditional girls-only Yuihime Private Academy is considering the possibility of starting to accept both genders and has thus made an agreement with a neighboring school to receive some of its students as an experiment to see the reaction to this adaptation. Shingo Iryu is one of the many students transferred for a ten month experimental phase at Yuihime Academy. He, his sister, and his fellow relocated colleagues are impressed by the sophisticated campus, but even more by the resistance of many students who don't want the boys over there.
When Ryou confesses her feelings to Tomoya he is initially reluctant to accept them, though upon further thought he decides to date her in order get to know her more. As the pair spends more time together Ryou is on cloud nine, but when rumors start to circulate about Tomoya and Kyou, the young girl’s bliss is short-lived. With Kyou repressing her feelings for the delinquent teen and sacrificing her own happiness in favor of her twin sister’s, Tomoya finds himself at the center of a complicated love triangle; but which girl has won his heart?
Death and reincarnation are inescapable, but what happens in between? Without warning and without his memories, a boy who only recalls his last name - Otonashi - wakes up next to a girl named Yuri who offers him a gun and tells him to shoot an angel. Assuming it must be a misunderstanding, Otonashi is then almost killed by the angel and is drawn into Yuri's army to battle to delay the beginning of his next life. Immortality is within reach, but if Otonashi remembers how he died, will he keep fighting or allow himself to vanish?