It I seems unlikely that Shay, as an Irish Assassin-turned-Templar, would be the Grandmaster for the French Templars, especially considering other videos seem to imply that Shay and Haythem are directly supporting the British Empire's interests in the New World during the Seven Years War. Theoretically, this would imply that they are also opposing the French Templar's plans.
Now, here's an idea: Shay is the driving force behind the purge that leaves old man Davenport the last of the Assassins in ACIII. Years after his hunt, Shay becomes a privateer for the British Templars against both Achilles' new Assassins and Haythem's playing-both-sides New World Templars, since Haythem turned on and killed his British benefactors between the wars. When Haythem dies, Shay finds himself with only one target left in the form of Connor. Connor, already an experienced privateer as well, also hunts Shay. The two men play a dangerous game of cat and mouse, and come to respect each other, as Shay sympathizes with Connors idealism tinged by the betrayals he's suffered, and Connor admires Shay's true devotion and focus to his cause. Thus, Connor recognizes that Shay "follows his own creed," while Shay sees Connor as the righteous combination of Assassin compassion and Templar order.
Your last mission is a massive ship to ship fight against the Aquilla, with its eagle themed look and captain named after wolfs, with the Morrigan, with its wolf themed look and captain named after a hawk, with both ships and warriors horribly wounded. Shay dies, but Connor bears a permanent mark from the fight, like a limp or a badass scar. Before he dies, Shay tells Connor of the chaotic forces brewing in both orders in France, and both men theorize on the hope of a "unified" Assassin-Templar alliance.
Cue a level in Unity where Connor arrives to help the frantic Arno and Elise, bearing the marks of his fight and encouraging their alliance in the memory of both his father and the man who hunted his brothers down.