- "Why endanger Templar blood when we have so many here that would see killing him as God's work?"
- ―William Stoughton defending his point to Samuel Parris, 1692.[src]
By 1692, he worked closely with Samuel Parris as an executioner. Having discovered that the Assassins Tom Stoddard and Jennifer Querry had come to Salem to hunt for a precursor artifact, Stoughton encouraged the Salem townsfolk to hunt and kill the Assassins, an idea that Parris objected.
They eventually caught up to the Assassins in a swamp and Stoughton let the injured Querry go so that they could follow her to Stoddard and the seer Dorothy's location. Stoddard, thinking that Jennifer was a traitor, attacked her. Stoughton took this opportunity to assault Stoddard and tied the trio up.
Stoughton tortured the Assassins for information and threatened to hurt the mute boy David, secretly Querry's son. The worried Querry then offered to give them information when Consus once again possessed Dorothy, much to the glee of Stoughton. Querry took upon the opportunity to kill a guard and free Stoddard when Stoughton shot her dead. The shocked Stoddard then tried to free Dorothy and David when Stoughton shot him in the arm.
The Templar threatened Stoddard and revealed that he was planning to experiment on the captured women to create more oracles. However, Dorothy, hearing Stoughton's words and overcome with guilt, killed herself in the fire. The enraged Stoughton tried to kill Stoddard, blaming him for the loss of his oracle and ranted on that he would find another even if he would try every woman in the colonies as a witch when his fellow Templar Samuel Parris interfered and shot Stoughton in the shoulder. Parris freed David and Stoddard as he clearly objected Stoughton's ways of violence.
- There is some confusion in between issues, and sometimes within the same issue, regarding which character is identified as Parris and which as Stoughton.