In Blast Factor the player pilot a microscopic craft through a series of infected cells and use the craft's weaponry to rid the cell of various infections.
The left analog stick moves the craft and the right fires the weapon (similar to Geometry Wars, Robotron: 2084, and Smash TV). Additionally, the player can violently tilt the SIXAXIS controller to the left or right to slosh the playing field to one side or the other, resulting in the infections being forced to one side, often grouping them for easier elimination. The player also has use of a Bio Magnetic Repulsor (B.M.R.) that triggers a time dilation effect and a force field that can be used to push away enemies. The B.M.R. recharges every 2 seconds in single player mode.
Each cell the player enters will have several infections appear. The objective to destroy all of the infections. The types and behaviors of the infections vary as the game progresses.
The player must cleanse 8 cells (or waves) in a specimen (or game level) to move on to the next specimen. There are various powerups to be gained, such as a Multi-Shot, Homing Super, and Super B.M.R.. The latter power up triggers a disruptive blast that destroys all enemies within range.
The player can increase their score by using the 'Blast Factor' of enemy explosions. Enemies caught in the destructive radius of an explosion will themselves be destroyed, giving an additional score bonus to the player. The score multiplier increases with each enemy destroyed in a chain of explosions.
The game has a self-modifying difficulty level based on the skill of the player. The difficulty is determined by changing the path of cells through each specimen. If the player does not die and completes the current cell within the specified time limit, the player is moved to the harder cell on completion. If the player dies, or does not finish the cell within the specified time limit, the player is moved to the easier cell. More points are awarded for completion of hard cells.
The end effect is an experience similar to a 2-dimensional space combat game like Blasteroids.