In History:In the Devil's Snare: The Salem Witchcraft Crisis of 1692 talks at length about John Alden's involvement in the witch trials. He was said to have been accused of being a witch by none other than Mercy Lewis! He was held in jail in Boston but eventually escaped and fled to NYC.
On Salem: John Alden (Shane West) returns from war to a town overwrought with panic. He begins to hunt witches and defend those he believes innocent and is blindsided when Mary Sibley, the woman he loved and left for the war, reveals to him her true identity as a witch.