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In that case I find kind of weird how Connor's obsession with Charles Lee actually increases during the last two sequences, while he just ignores Washington after that reveal. That's probably why I found the whole thing confusing.
To be fair, Charles is a Templar, Washington is not.
Aren't the Freemasons an extension of the Templars
One of the database updates after the Haytham-Washington scene confirms that Washington was behind the attack on his village.
It is just another problem with this games storyline, one of many.
The entire game post final fight with Haytham was very abrupt and poor. Lee was just a plot vessel to explain the key. And the more the series progresses the more the bad sci fi ruins the good historical fantasy.
The clouds pass... the rain does its work and all individual beings flow into their forms." The Book of Changes
It never clearly states he's responsible for the attack that killed Connor's mum. It claims he has commited these attrocities, but never explicitly states he did this one.I believe it's left intentionally vague, a sign of the Templars doing there job very good.
I store dead bodies all up under my house and every night I hear them runnin' they mouths.