In June 1692, Stoddard arrived in Salem Town after travelling fromLondon on assignment to locate a Piece of Eden. After witnessing the hanging of Bridget Bishop, he went to meet with his contacts in the city, who turned out to be Templars in disguise. He was then joined by his real contact, Jennifer Querry, who explained the history of the strange 'illness' that had been plaguing Salem, and the involvement of the Templars Samuel Parris and William Stoughton.
The two Assassins later infiltrated a warehouse in order to track down the Piece of Eden. Finding a dungeon underneath the warehouse, Stoddard was forced to free a young girl named Dorothy Osborne and a mute boy named David, with the latter's promise to lead the way to the artifact's location. Unconvinced, Tom threatened Dorothy as he pushed the mute boy away. Jennifer and Dorothy eventually managed to calm him down. However, Dorothy suddenly fainted and recited Tom's father's last words from Dante's The Divine Comedy. As Jennifer went to the young girl's side, Stoddard had to defend the trio from an onslaught of attackers.
Querry eventually discovered an exit and Stoddard set the basement aflame as they escaped to the swamp. Seeing Querry's inability to carry the mute boy, Stoddard told David to go to Ipswich for a man named Arbour and gave him a feather. Querry disagreed and Stoddard tried to explain that the boy was slowing them down and endangering Dorothy's life, to no avail. However, there was a loud bang and Stoddard saw another wave of attackers. He was forced to leave an injured Querry and David for the girl's life.
Dorothy, again possessed, revealed herself as Consus and spoke to Charlotte de la Cruz who was reliving Tom's memories. Confused, Stoddard questioned Dorothy but the girl was back to herself. She told him that he would have a family and blamed him for leaving Querry and David. The pair eventually reached the dock and Stoddard was surprised to see Templars arrive.
Querry suddenly appeared and told him that she left the boy for Tom's greater good. Thinking that she was lying, Stoddard attacked her as Dorothy tried to defend Jennifer from him. However, they were suddenly assaulted by Templars who followed Jennifer and tied them up.