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After Sequence 5 and the infiltration of Abstergo, William finally opens up to Desmond and apologizes for his behavior, saying he was never very good at being a father. They talk on even terms, and Desmond even asks after his mother.
Haytham and Ziio's last scene together before game switches to Connor's story. Ziio reaches out and grabs his hand and when Haytham is rather clumsily trying to be a gentleman and leave before it goes any further she just kisses him.
After taking him in, Achilles gives Connor his English name. It appears at first he chose "Connor" because his actual name sounds slightly like it, but then, if you look at the two graves behind the manor you see that Achilles had a son by that name who died the same year as his wife. Suddenly, the significance of the name takes on a much deeper meaning.
When Haytham tries to smuggle Connor into a Templar house, the guard at the door acknowledges him but "not the savage". Haytham's answer is quick, simple and honest in its execution and comes very early on after the father/son reunion from which Connor is still sour, making it even more heartwarming.
"He is my son."
What makes this scene even better is Connor's shocked expression at his response, considering how their relationship has been going thus far.
Haytham's death. While not exactly a model father, he does have a small So Proud of You moment before he draws his last, and gives him the closest thing to a compliment as the man is probably capable of bestowing considering the circumstances.
"Still, I'm proud of you in a way. You have shown great conviction. Strength. Courage. All noble qualities... I should have killed you long ago."
Easy to miss, but during an early out-of-Animus moment, if you take the time to make Desmond speak to Rebecca, at one point she will discuss with him Subject 16, at which Desmond will immediately cut her off and state; "His name is Clay." After all this time, and what Clay went through, somebody finally has recognized him, his sacrifices, and treated him as a human being, rather than a lab experiment gone wrong.
A blink-and-you'll-miss-it moment, but in one Boston Liberation mission, Connor (who has been passing as a settler of Mediterranean heritage to explain his skin colour,) introduces himself to one of the Patriots. The man says that "Connor" is a fine name for a Welshman, and asks what Connor's real name is. Connor gives his real name, which is quite obviously Native American, and without hesitating for a moment the man calls it "a good strong name" and tells him he should use it more often. Considering how much attention is drawn to the fact that the average Patriot's values of "freedom" and "equality" only apply to the settlers, it's great to meet someone who believes those concepts apply to the Natives as well, and doesn't have to think twice about it.
Said man becomes an Assassin recruit once you finish that chain of Liberation missions, and it turned out he was the child who watched Haythem kill the man in the opera from the very first mission. He even mentions that he knows for a fact it was Connor's father who had done the killing, implying Connor is sharing personal information with his recruits off screen, and apparently none of them begrudge him for having a Templar as a father, not even the one who lost an uncle to the man.
The Homestead missions are a chain of CMOH in increasing order of intensity, with things like hooking up a couple, helping a mother deliver her baby, and driving off the abusive husband of another woman. Designed to bring feelings of warmth and fuzziness.
Of note is the conclusion of Norris and Myriam's line - Ellen has created a flag for the homestead, giving it to Connor.
The look on Connor's face and the genuine happiness in his voice when Norris announces that Myriam agreed to marry him. Given that Connor's life tends towards some combination of The Woobie and The Chew Toy, the fact that his face lights up proves that it's not all miserable.
And then he gives Myriam away at the wedding.
The Quebec assassination contracts, to a curious degree. For example, the mission "The Quebec Act." Stopping the tyranny that the act has on the people of Ohio, right? Nope; the objective is preventing hostility between Ohio and Quebec. Overall, the missions emphasize that Quebec and other northern holdings are A) not part of the Thirteen Colonies and thus not tied to their issues, and B) they do not want to kick the British out. In a meta sense, it's nice for Canadian players who don't want to be portrayed as part of the Not Evil, Just Misunderstood antagonistsnote having Stephane and Norris as Canadian allies further alleviates such fears. Furthermore, it provides in-story precedence for a major difference between the Assassins and Templars; Assassins may support freedom, but unlike the Templars, they don't force their views on the unwilling.
'Course it should be mentioned that the developers are based out of Montreal and are at least partially made up of Francophone Canadians; it's not too surprising they portray Canadians positively.
After the signing of the Declaration Achilles and Connor have a little talk where Achilles admits he's proud of all that Connor's accomplished so far. Connor, touched and surprised, asks if that was a compliment.
Connor's reaction to seeing his very-much-alive mother in The Tyranny of King Washington. Connor, always stoic and serious, smiles—a real smile—and actually hugs her. Everything promptly goes to hell from then on.
We have another dose of this in Episode 2 where he reunites with Kanen'to:kon, who is now working with the rebels and Sam Adams. Not only that, but he actually lives till the end this time, which means we get to see him in Episode 3.
After Ben Franklin is freed from the Apple of Eden's influence, it's touching to see the lengths he's going to atone for his sins and especially how concerned he is about Connor during "The Redemption."