Shoot the Bullet works like a normal danmaku game, with one main difference. You still have to dodge bullets that are thrown at you, but you are unable to shoot at the boss to deal damage. Instead, you must use Aya's camera to take a certain amount of pictures of the boss. To assist the player, Aya's camera is capable of eliminating all of the bullets within the viewfinder when a shot is taken, even if the boss is not within the photo. The shot is considered successful when the boss is featured in the photo, and it will be given a score based on certain criteria including the amount and type of bullets in the photo. The bosses included in this game come from the games Embodiment of Scarlet Devil to Phantasmagoria of Flower View.

In Shoot the Bullet, you play as Aya Shameimaru as she photographs the bosses from various Touhou games. However, no one ever reveals why she is taking these photos. In fact, at one point it is pointed out that "No one knows the purpose of the photos, except Aya", and the only reason she does not shoot the opponents is "not to be nice, but because she doesn't want her bullets in the picture."