Character Mode is the primary mode of play when the mission switches focus onto the main character once they have left their vehicle and entered a Gate. Each game's Character Mode is named after its respective main character (ie, Jason Mode, Roddy Mode).

In Character Mode, the camera zooms in on the player character and gives them access to new weapons and abilities as they explore catacombs. Excluding Blaster Master: Blasting Again and Blaster Master Zero, bosses can only be encountered in Character Mode. In Blaster Master, Enemy Below and Overdrive, the camera changes to an overhead view and allows the player to move in all directions. Roddy does not control much differently from Sophia J-7 in Blasting Again, but he does face new challenges and obstacles.

Blaster Master 2's Character Mode is an inversion, as Gates lead directly to boss arenas, and Jason loses several abilities while in this mode.

There is a variant of this mode in Blaster Master Zero called EX Character Mode. However this is only accessable if the player has gotten the DLC characters Gunvolt, Ekoro, Shantae and Shovel Knight. In this mode, players select one of the aforementioned characters and play through the game with them. Where they drive a Sophia III recolored to match their palette and use their abilities from their games when outside the vehicle. They are also unable to use the sub weapons Jason uses. Though they still must be obtained in order to access Area 9