In 1754, the Templar Haytham Kenway arrived in Boston to locate a Precursor site. He enlisted the help of Charles Lee, William Johnson, Thomas Hickey, Benjamin Church, and John Pitcairn to aid him in his quest. During the Templars' search, they stayed at the Green Dragon Tavern. Haytham sought to win the trust of the Kanien'kehá:ka to locate the site, and began this by freeing natives enslaved by Silas Thatcher at Southgate Fort. A year later, after Kaniehtí:io led Haytham to the site, Haytham returned to the Green Dragon Tavern to induct Lee into the Order.
In 1770, Haytham and Kaniehtí:io's son Ratonhnhaké:ton traveled to Boston with his mentor Achilles Davenport to buy supplies for their homestead. During the trip, Achilles chose "Connor" to be the boy's alias. After purchasing their supplies, a protest began outside the Old State House. Connor spotted his father and was ordered to follow his accomplice onto the rooftop. Connor stopped the man from firing his rifle, but on the opposite roof, Lee fired a shot, prompting the British soldiers to fire on the crowd. Haytham spotted Connor and pointed him out to a Grenadier, forcing Connor to flee. Samuel Adams later found Connor and helped him escape the city by advising him to tear down his wanted posters and showing him how to bribe town criers and printers, before taking him through the Freemasons' tunnels to a harbor.
In 1773, Connor returned to Boston to find William Johnson, as the Templar was seeking to purchase the land where Connor's village was located. Adams and William Molineux informed him of the tea taxes Johnson was exploiting to gain the money for the purchase, so Connor blew up Johnson's smuggled tea before participating in the Boston Tea Party, where he helped in the dumping of multiple crates of tea into Boston Harbor. In the meantime, he recruited Stephane Chapheau, Duncan Little and Clipper Wilkinson into the Assassin Brotherhood. Connor would also go on to collect more of Ben Franklin's almanac pages within the city.
In 1775, Connor aided the Sons of Liberty once again to find John Pitcairn. He met with Paul Revere at his home in Boston before the Midnight Ride. Connor eventually assassinated Pitcairn at the Battle of Bunker Hill, outside Charlestown, north of Boston. In 1782, Connor tracked Charles Lee to Boston and chased him through a shipyard. Both men were wounded and rendered unconscious during the chase, but Lee managed to regain consciousness first and take a ship to Monmouth.
In an alternate reality projected by an Apple of Eden, Ratonhnhaké:ton was imprisoned in Boston by the Bluecoats of King Washington. With Kanen'tó:kon's help, he managed to escape and join up with Samuel Adams. After nearly killing and reluctantly freeing Benjamin Franklin from Washington's thrall, the trio laid their plans for assassinating the tyrant. They fought their way to a ship in the harbor, and from there they set sail to New York.