Bad Apple Wars has two methods of story progression: selecting a location (which is color-coded so as to hint which love interest you might find there) and Soul Touch. This makes it relatively straight-forward compared to other otome, such as the choice-heavy Amnesia: Memories or the occasionally time-sensitive Norn9: Var Commons.
Each route has two possible endings: a good ending and a NEVAEH ending. Both endings must be seen in order to unlock trophies. The available routes are as follows:
- Alma: The red-haired leader of the Bad Apples. This can be considered the game's main route, and is therefore first in the recommended order.
- Higa: Alma's right-hand man. Higa is incredibly loyal to the man he sees as his "aniki" (big brother), and by extension, the Bad Apples.
- Shikishima: An "odd apple" aligned with neither side in the war. Despite his non-allegiance, Shikishima's route can only be accessed by aligning with the Bad Apples.
- Satoru: A boy who enters NEVAEH Academy on the same day as Rinka, though all he does is study. Like Shikishima, he is not aligned with either side, though his route can only be accessed by aligning with the Prefects.
- White Mask: The mysterious leader of the Prefects. Rinka does not know his name or anything else about him.