In the first appearance, at an unspecified time, Mather was a seeker of beings gifted with magic powers. The Dark Rider (a powerful magus of a pre-historic Era) found him, plagued him, and forced him to serve for his own purposes: to find people with magic powers to feed of their power.
The fanatic Cotton Mather started his mission for the Dark Rider. He arrived at Salem, Massachusetts in the Winter between the 1691 and the 1692 with the purpose of increasing the fear of witchcraft in people in order to find real witches (or to cover the Dark Rider activities). Mather increased the fanaticism of Salem's people , had the Reverend John Burroughs killed by hanging, and fomented the witchhunt. Cotton Mather traveled in the 20th century (probably helped by the Dark Rider) to the Castle of Doom in Laveria. With his "voice" he attracted the Scarlet Witch to the Castle and captured her.
Spider-Man was transported to the Castle by a Scarlet Witch's spell. He tried to stop Mather, but was defeated by his "fire" and by the Scarlet Witch, controlled by Mather. Mather used Dr. Doom's Time Machine and brought Wanda back to 1692 where he exposed her to a public pyre. The Dark Rider started to absorb Scarlet Witch's magic powers. During the execution Mather was assaulted by Vision and Spider-Man, who had followed him to Salem using Doom's Time Machine.
In the second appearance of Cotton Mather, the crowd overpowered Spider-Man and Scarlet Witch, and Cotton Mather knocked the Vision down with his "cross-fire". The heroes were imprisoned. Spider-Man and Vision freed themselves. Mather met the Dark Rider in the wood near Salem. The two were assaulted by Spider-Man and the Vision. Dr. Doom arrived on the scene attracted by Dark Rider's power and the foolish Mather greeted the coming of the Avenging Angel.
Cotton Mather saw the Angel of Light in Dr. Doom, come to fight the darkness in Man and declared himself servant of the new "master". Mather asked Doom to show him the way of the Light and to be taught how to cleanse the world from evil. Dr. Doom hurled him away. The Dark Rider absorbed more power from the heroes and in particular from Dr. Doom's latent black magic powers and managed to defeat him, the two Avengers, and Spider-Man.
The Dark Rider set up machinery to absorb the powers from the four heroes. He thanked Cotton Mather for his optimal service. Then Mather was forced by him to take the Soul Blade, a shining knife, to be used to kill the heroes and to transfer all their power to the Dark Rider. Mather was about to stab the Scarlet Witch, but was stopped by Moondragon, transported there by Wanda's last spell. Moondragon held the Dark Rider for the right time to let the other heroes awaken and fight together against the demonic menace. The heroes defeated the Dark Rider who burnt into cinder in front of Cotton Mather's eyes. Cotton Mather went mad. His mind could not bear the events of that night. Cotton Mather, now mad, screamed while Spider-Man left the 17th century on the Time Platform.
In the finish of his story, Cotton Mather tried to tell the history of the Dark Rider and of the battle he attended, but no one believed him. He was believed insane.
Mather powers' origin are unknown (probably they were granted to him by the Dark Rider). Mather could sense and find magic beings, project his voice (or thoughts) at very long distances, control and command other's will by touching them or hitting them with the fire shot from his wooden cross. Mather seemed stronger than a normal human. Mather used a wooden cross as weapon. The cross could shoot a "purifying" fire, not burning things, but strong enough to hurt Spider-Man and drive the Vision off. The fire also allowed him to control Scarlet Witch's will.