While his Mentor caught up with an old friend, Shay joined his fellow Assassins for a training session. Shay set out with Liam to pursue a lead regarding the location of the stolen Precursor box and Manuscript.

Shay and Liam pursued the high-ranking Templar Lawrence Washington, in an effort to recover the stolen Precursor box and Manuscript.

Shay and Liam set out to meet with one of their allies, who had information on the whereabouts of the Templar Samuel Smith. Shay and Liam journeyed to Albany to track down the Templar James Wardrop and recover the manuscript that was in his possession. Shay traveled to Sleepy Hollow, hoping that the scientist Benjamin Franklin would be able to activate the Precursor box. Shay was tasked with the retrieval of a Piece of Eden supposedly located in Lisbon.

Following the disaster in Lisbon, Shay went to confront his Mentor at the Homestead.

After several weeks of languishing at an unknown location, Shay tried to piece together what happened. Shay returned to the Finnegans' residence, where he received a new task. Shay and Christopher Gist reunited with Colonel George Monro in Albany. With new information on the gangs' activities, Shay returned to Colonel Monro to see what might be done.

Shay discovered Colonel Monro was in trouble and decided to come to his friend's aid. Having rescued Colonel Monro, Shay met with his Templar allies, who informed him of Kesegowaase's next attack and their plan to combat it. Having sailed to Albany, Shay and his first mate Christopher Gist found the city in turmoil, with Colonel George Monro's troops clashing with Kesegowaase's forces.

Following his official induction into the Templar Order, Shay was given his next mission by Haytham Kenway, Grand Master of the Colonial Templars. With Adéwalé back in the colonies, Shay and his fellow Templars decided to track him down and eliminate him.

Shay and the Templars focused on taking down the Assassin-affiliated gangs that plagued New York. With the British Army on the Templars' side, Shay set out to locate Hope and assassinate her.

Shay set out to uncover the destination of Chevalier's expedition. With Chevalier's encoded maps in his possession, Shay consulted James Cook to uncover the destination of the Assassins' expedition. With the destination of the Assassins' expedition revealed, Shay and his fellow Templars set out to prevent Liam and Achilles from finding and activating the Seismic Temple.