The player's main method of attack is their shot, but they also have access to a limited number of spell cards (also referred to as bombs), whose exact properties depend on the character and shot type, but all spell cards will clear the screen of bullets, grant the player temporary invulnerability, and deal a large amount of damage.

Unlike its predecessors Mountain of Faith and Subterranean Animism, bombs are given their own counter, rather than being attached to the player's shot power.

The game features three playable characters, Reimu, Marisa, and Sanae, each of whom have two shot types, one of which deals high damage, whereas the other has homing projectiles.

In the Extra Stage, Marisa notices that the UFOs appear to be housing small snakes, which was the result of Nue Houjuu attaching the Seed of Unknown Form to them out of boredom.

Undefined Fantastic Object was announced on ZUN's website on 26 February 2009,[6] and the full game was released at Comiket on August 15.