The section below of the guide contains a walkthrough for Welcome to Boston, a mission that opens up the second sequence in the game.
After landing in Boston, follow your companion.
He will eventually leave you. Turn on the map and head to the marked spot.
There you will meet Benjamin Franklin, who will give you an additional mission of collecting the lost pages from his almanac. A description of their locations can be found in the chapter of this guide dedicated to collectibles.
I'd recommend taking care of that later on and for now enter the nearby shop to buy a sword and a pistol.
Equipped with them, you can get onto a horse and head to the "Green Dragon" inn with Lee, where on the upper floor you will meet William Johnson.