God Eater Online takes place in year 2075 after God Eater 2 Rage Burst in the Fenrir's Himalayan Branch. Medium and large-sized Aragami are beginning to appear around the Branch in a pattern that was similar to what happened when the Branch was destroyed in the past. The God Eaters at the Branch have to fend off the Aragami while investigating the ruins of the old Branch for answers.
The Director of the Branch requests Fenrir HQ for assistance, but receives no reply. He then flees the Branch, leaving the God Eaters stranded. Godot then names himself the Acting Director and the Protagonist as 1st Unit Captain in his place.
It turns out that the ruins of the old Branch was in fact a research facility. At the same time, the Aragami are congregating and fusing into a single organism of very large size.