Three years after the event in God Eater Burst, a new fatal pandemic called the Black Plague caused by red rain has struck the Far East area. Members of Special Forces Blood, an affiliate of Fenrir who reside in a mobile base, are sent to assist.
After going through the various events at the Fenrir Far East Branch, Alisa develops a feeling similar to respect for 1st Unit leader, Yuu. Meanwhile, Alisa and Yuu are dispatched to Aegis Island on a protection mission.
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