The main goal of the game is to defeat a dangerous group of creatures known as the Malicious. There is no actual stage progression in Malicious. Instead, all stages start the player off directly in big fights against a boss and his subordinates.

For weapon, the player makes use of a special black cloak that hangs from the main character's neck called the Cloak of Ash. The cloak, created using technology from the great prophets, changes into a variety of forms. As an example, the cloak can becomes a fist for close range melee attacks. It can also become a projectile weapon, making use of "demon bullets" to target multiple enemies with a lock on.

The cloak can also wrap around the character to guard against incoming attacks.

The player is able to freely select whichever stage to come next. The ordering could be important, as defeating a boss gives the character that boss's powers in the form of a new action. The character also gains power in other areas, including increased jump height and the ability to lock on to a greater number of enemies with "demon bullet" blasts.

As the player takes damage during the game, parts of the main character's clothes and body will disappear. However there are certain places where the player can get healed up when certain conditions are met, which will restore the missing parts of the main character's body (clothes, however, can't be restored.)