Having lost his mother in childbirth and years later his father to the sea, Shay wallowed in self pity on the streets of New York. A chance meeting with his childhood friend Liam O'Brian offered up a chance to join the Brotherhood.

 

With four years of training under his belt, including successful missions to acquire two First Civ artifacts, Shay is sent on a mission to Lisbon. It ends in disaster bringing about the destruction of the entire city. Unset with his mentor Achilles, Shay vows to never again take an innocent life, and, after stealing the journal from Achilles, a clifftop confrontation ensues. 

 

Awaking in New York, Shay quickly goes about ridding the city of it's gangs with the aid of George Monro, who unbeknownst to Shay, is a Templar. Finding that their philosophies aline, Shay spends the next few years aiding and eventually joining the Templar Organisation. Along the way, Shay learns that it is his old friends in the Assassin Order that have been helping the gangs in New York and vows to hunt them down if they get in his way. 

 

After informing him of the box and it's destructive capabilities, Shay and Haytham come to the same conclusion, they must relieve the Assassins of the artifact. In doing so, Shay tracks down and kills the remaining members of the Assassin Order, including the Legendary Assassin Adewale. 

 

They eventually learn that Achilles and Liam are in a First Civ temple in the Arctic, where a final confrontation ensues. Shay is forced to kill his friend Liam but manages to persuade Haytham to spare Achilles, leaving him a cripple. Haytham then entrusts the retrieval of the box to Shay.