The story of Blue Seed 2 OVA takes place after the TV series.
Susa-no-o has returned once again to ravage the city, and it's up to the Terrestrial Administration Center to stop it. Momiji and Kusanagi's relationship is on the rocks; the rest of the TAC is scrambling to get things together so they can effectively wipe out Susa-no-o. A mysterious girl, claiming to be an Aragami like Kusanagi, is causing chaos for the TAC and Momiji as well. Will they be able to pull together in time?