(Tellemicus' Note) Please keep in mind that I came up with this idea BEFORE AC3: Tyranny was released.
The Empire of America (story series)
Haytham's Expedition
Book 1—1756-68
When he's sent to America, Haytham Kenway brings the Apple of Eden that the Templars had taken from Elizabeth I. With it and the Key, he's able to open the Grand Temple. Inside, he meets the furious 'spirit' of Juno who orders him to leave her sanctum, which he calmly accepts. He returns later with a large force of Templars who set up an outpost near the Grand Temple so that they can more easily study how the technology works. Though he did valiantly attempt to prevent it from happening, his Templar underlings took it upon themselves to drive the Kanatahséton from their lands (including the pregnant Kaniehtí:io). Later, they set up a new fortified headquarters in the ruined and rebuilt village. Many of the Kanatahséton were given refuge within their neighbor Iroquois tribes, where Ratonhnhaké:ton was born and raised.
During Connor's childhood, the Templar Order was busy researching the secrets within the Grand Temple. Many Templars were disgruntled to learn there were no weapons of mass destruction, no mystical Pieces of Eden, or anything immediately useful to them and their limited technology. But they were quite disturbed to learn about the Earth's impending destruction from a massive burst of fire from the sun. At the same time, they also learned that the Grand Temple housed the very device necessary for protecting the world from the solar flare and preserving humanity. Realizing that they needed to maintain control of the Grand Temple until the destined date, the Templars built a large military citadel around the site.
Ratonhnhaké:ton's Journey
Book 2—1769-75
When he was 13, Ratonhnhaké:ton grew impatient and angry at the fact that his people had been driven from their lands and that none of their warriors were able to do anything more than annoy the Templar invaders. Following advice from his mother, Ratonhnhaké:ton sought out Achilles, but all he found was the man's corpse and a deteriorating mansion. Inside the mansion, he found Achilles' Codex, weapons, and what little intelligence on the Templar Order he had managed to retain after his banishment by Haytham. Seeing an unique opportunity, Ratonhnhaké:ton returned and was able to talk a number of his people to join him in rebuilding the mansion and restarting the Assassin Order after he and his mother managed to decode the Codex.
For the next five years, Ratonhnhaké:ton (who took the name of 'Connor' after Achilles' deceased son) and the volunteers of his people were able to gradually rebuild and revitalize the decrepit mansion and bring new settlers to the growing homestead. Connor and his people were also very busy learning and perfecting the techniques, weapons, and knowledge of the Assassins and trying to understand the Templars' goals. Connor was even able to get Robert Faulkner to repair the Aquila and get started on sea missions again. As more and more successful business began to flow from the homestead, more and more of the Kanatahséton people began to arrive and settle the land…and more Assassin recruits began to enlist (both among the Kanatahséton and the settlers)
Origins of the Revolutionary War
Book 3—1760-75
After the French and Indian War, Haytham saw the amount of influence that Washington garnered from the people and he wished to turn the man into a puppet of the Templar Order, if not have him become a Templar entirely. He had Washington transferred to the new Fort Grandeur on former Kanatahséton lands. During his stay there, Washington was Haytham's personal assistant and bodyguard. Using the Apple of Eden to control and entice Washington with the hunger for greater power, Haytham turned him into an ideal Templar associate (1760-68). Thus, when the American Revolutionary War broke out (1772) and Washington was named Commander-in-Chief, the Templars had the perfect puppet for controlling the war. With help from various Pieces of Eden, Washington was able to lead the Patriots to numerous victories and crushed the Loyalists and Regulars. Washington was hailed as an unconquerable war hero among the Patriots and was easily elected to become the new leader of America once the British were forced to acknowledge the Colonies as their own independent nation (1775). Washington took up the title of Emperor of America and took New York City as the capital of America.
Return of the Assassins
Book 4—1775
Having remained largely outside of the conflict due to having no allegiances to either side, the Davenport Assassins (as the Kanatahséton had renamed themselves) finally were drawn out of their isolation. This began when tax collectors for Emperor Washington came to the homestead, seeking the taxes that they felt were owed to the federal government. The homestead rebuffed the accusations, claiming to not view Washington as their ruler. When the tax collectors started getting violent, the Assassins struck back, killing all but one to carry a message back to New York to leave them in peace. Secretly, a group of Assassins led by Connor followed the messenger to New York City, hoping to at least get a measure of what they were up against.