User blog comment:TheDarkKnightHasRisen/Connor: The child, the apprentice, the Assassin/@comment-3446336-20121008040238/@comment-4889347-20121009055726

Well, Forts in the game are acting as Templar Dens in the previous dens. We can safely assume that around this time Connor is siding with the Colonists. Connor putting up the Thirteen Star Flag is another way of signifying that it's Assassin Territory. Also, Colonists needed some larger bases. I have a feeling that Connor will mainly side with colonists in the beginning, and near the end they'll betray him.