Baroque is a post-apocalyptic survival horror manga. It is told from the view point of a nameless protagonist without any memories and a fleeting ability to speak. It begins when the protagonist wakes up into a distorted world with a red sky. He soon finds variously mutated beings, vaguely resembling humans, living in a ruined city, and is told by them to visit a place known as the Nerve Tower. He is temporarily joined by a red-eyed human figure known as Archangel, who wears false wings on his back. Archangel informs him that it is the protagonist himself who caused the world to become distorted in an incident known as the Great Heat Wave some time in the past.
Archangel arms the protagonist with a unique sword and large gun, informing him that the God of their world is a literal being who physically exists and has been driven into insanity. The Mad God's existence is believed to be the cause of the world's mutations, as anything that travels too close becomes grotesque and deformed. As the Mad God dwells within the deepest chamber of Nerve Tower, the constantly shifting matter around has questioned the stability of the tower itself.
The protagonist is told, to repent for his sins, he must "Purify" the Mad God by firing a special gun into it (An over sized, shoulder-mounted revolver). Before doing so, he must traverse through various mutant creatures, called Grotesques, within Nerve Tower in order to reach its lowest chamber where the Mad God resides.