Echinacea

Main character notices his always reserved female classmate Amamiya walking alone in the park. The next day he decides to follow her after school to see where she is going. She is approached by flying men who want to avenge their blown up companion the other night, so they attack. Amamiya wins this fight, but loses consciousness. Protagonist takes her home and learns that she is an android with a mission in this town, and those flying men are also androids dispatched to prevent her from doing that. Amamiya asks for cooperation in fulfilling her mission, and boy agrees as the alternative is memory erasing with unclear consequences.

[From vndbreview]