User blog comment:Subject 9/Colonial Assassins 1754-1763/@comment-1153722-20130315195814

Achilles, Agaté and Aveline were not part of the same Assassin Brotherhood. Achilles was the Mentor of the Brotherhood in the British American colonies, Agaté was the Mentor of the Brotherhood in Louisiana. They are different branches. Same with the Templars in both regions.

And I don't believe it's ever said that the Colonial Brotherhood of Assassins was the most powerful branch, just that it was a powerful branch. It also speaks of an Assassin 'witch hunt', so I don't think the Templars just attacked all Assassins at the same time and stood victorious. They are never specific on what happened, so everything is speculation. The Colonial Templars had a lot of henchmen too, and did not consist of just the ones that Connor killed.

But yes, the Templars did not know that there was any Assassin left, as both Thomas Hickey and Charles Lee explicitly say.

As for the Assassins 'siding with the Indians', Achilles' database entry talks of how he tried to forge an alliance with the Kanien'kehá:ka. Some deleted dialogue talks about how Achilles knew Connor's mother and that she was an ally and a friend. This is deleted for a reason, but obviously the story behind that passage from the database entry.