As a highly skilled assassin, although one young and somewhat naive, I would imagine Connor would have been one of the most efficient Templar agents of all history had Haytham managed to convert him to their cause. In fact, I'm shocked he didn't revert to more extreme measures in order to recruit his son.

So, during their time together, Haytham starts off small, telling him half-truths and lies about Connor's mother and why he defected from the assassins. Maybe he goes so far as to gaslight Connor about what happened with his village and their previous almost-encounters. He plays Lee off as a pawn. Discovering Washington's orders regarding the Iroquois nations is a stealth mission, Haytham didn't know exactly what George had ordered, but it's lucky they set off to find the incriminating evidence as soon as he heard something was going down, wasn't it?

Soon, he starts using more torturous methods to convince Connor that he's right. Emotional abuse is played off as just cultural differences, being desperate to save people from themselves, trying to make others see Connor as he is and not as a savage, those are the real reasons Haytham seems mean, there's no manipulation going on, honestly...

To prove his point about order and control, about how free will is evil, he sets a couple of sadistic rapists on his son- those men hurt so many women in the same way, isn't it lucky Daddy happened to be nearby? How terrible it is that he was just a bit too late to stop them. Aren't people just so horrible? Connor's kindness and respect for people is rare, if only everybody were more like him... Oh, but they can be, with just a little nudge.

And slowly, but surely, Connor is indoctrinated into the Templar order, and by the time the Assassins and their allies know what's going down... well, it's a bit late.