Connor Finds out His Father's Identity (Spoiler if You Haven't Begun the Game)
I'm definitely one of the site members who is the furthest behind in the game (only finished Sequence 5), but have a question for those who might know better.
After Achilles is done telling Connor the story of the history of the Assassins, the two go down to the hidden basement, where the wall with the Templars is kept. At this point, Connor says something to the effect of, "And all of them must die, including my father." I really was surprised at two things during this scene. First was the fact that he had no reaction to the picture of Charles Lee and second that he nonchalantly referred to Haytham as his father.
So, my question is, do we know definitively when he learned his father's identity? I thought that during the loading screen where you control Ziio, she makes it apparent that she wanted to steer clear of Haytham once she learned his true identity, but it's also made clear that she could never become (forgetting the name of the position) within her tribe due to Connor's father. So did she tell Connor who his father was? Did someone else in the tribe? Did Achilles do it in the story? If so, how would he have known if Ziio stayed hidden following Connor's conception?
It's quite possible I missed something in a conversation, but I was shocked that Connor knew his relationship to Haytham when the wall was revealed.
Thanks in advance for the help.
It was never made clear how he knew of his father. And it will get even more confusing later in the game. 
Once you've finished the game, you should check out the threads we've made that already covered this and other related topics.
I'll post my "this makes the most sense to me" theories when I get home for everyone to read... Method has already heard them in chat with me earlier though.
“Force has no place where there is need of skill." Herodotus
Like 90% of the things in this game, everything is assumed. We can assume that Achilles and Haytham have a history because Ziio trained under Achilles when she was young. Through that, she learned what Order Haytham belonged to. I'm sure that Achilles mentioned these things to Connor during "story time."
Things we know:
1 – Ziio knows Achilles – as per Clan Mother speech – “... he will help you as he helped your mother.”
2 – Ziio figures out Haytham is a Templar – as per her soliloquy
3 – Ziio keeps baby Connor secret from Haytham and keeps his influence away from baby Connor– soliloquy
Things we don’t know:
1 – How Ziio knows Achilles. Was she actually trained as an Assassin? Was he her safe haven from Haytham when pregnant? Both?
2 – Did Ziio know Haytham and his merry band of not-so-gentlemen were Templars before they met?
3 – Did Ziio keep Haytham secret from baby Connor?
Cheese’s Cheesy Speculation (what makes since to me – and how I want it to be, haha):
Firstly, I think the Clan Mother knows more than she lets on about the Assassins and Templars. She seems to know the land must be protected. Other tribes do sell their land to the intruders, but she knows they mustn’t.
I think Juno appears to Ziio to let her know that she must protect the land. If nothing else, Juno needs Ziio in place to meet Haytham and give birth to Connor ultimately leading to
Timeline that makes sense to me (and how I surmise it all went down):
1 – Ziio finds out land must be protected in similar spirit quest as Connor. Seeks out Achilles.
2 – Ziio trains for a little bit under Achilles before meeting Haytham. Perhaps they tried to elucidate some of the Templar Order, perhaps not.
3 – Events transpire wherein Ziio and Haytham bump uglies and Ziio conceives baby Connor, forcing Ziio to abandon the remainder of her training for the time being.
4 – Ziio realizes Haytham is a bad guy and confides in Achilles, hiding out on the homestead so word can’t get back to Haytham that his Mohawk Strange is with child.
5 – Ziio and Achilles continue to build their Big Board of Achilles’s Heels, finding out as much as possible about the Templar Order and plans, but unable to do anything as an old geezer and a pregnant chick.
6 – Ziio returns to Mohawk village and has baby Connor. Raises small child and never returns to Achilles (leading partly to his severe cynicism about conquering the Templars).
7 – Ziio tells baby Connor about his evil rape-daddy, and how he’s a bad, bad man, but never tells baby Connor who Haytham is. Just that he is a strong and powerful man whose only goals are to control others and force his kind of peace.
8 – Shit goes down. Village burns. Baby Connor meets Charles Lee. Baby Connor finds Achilles.
9 – Achilles never tells baby Connor his father’s name, but upon seeing the wall of Achilles’s Heels, he puts it together and says aloud, “Even my father.” I think he realizes on his own. Also, could be similar to Lord Vader sensing that Luke is on the next ship via the force.
10 – Throughout training and story time, Achilles tells baby Connor about the type man his father is.
Things I don’t think make sense:
1 – A history between Haytham and Achilles pre-AC3. Haytham didn’t come to the Americas until the beginning of the game. I think Achilles was born, or at least spent much of his life, in the colonies. Their paths likely never met before the events that transpired in AC3.
2 – I don’t think Ziio knew Haytham was a Templar until after the conception of Connor. I thought she said that she realized his ways in her soliloquy.
tl;dr version:
I think Ziio tells baby Connor ABOUT his father, but not who it is. I also don’t think Achilles tells him. I think Connor puts it together when he sees the Wall of Templars. I then think Achilles tells him about the type of guy his father is afterward.
As always – Feel free to correct me if I'm wrong.
“Force has no place where there is need of skill." Herodotus
Like 90% of the things in this game, everything is assumed
This is a contradictio in terminis.
1 – Ziio knows Achilles – as per Clan Mother speech – “... he will help you as he helped your mother.”
I never got that at all, after two playthroughs of the game. I'll have to go back and watch that scene again, but I don't recall it mentioning any connection between Connor's mother and Achilles.
3 – Ziio keeps baby Connor secret from Haytham and keeps his influence away from baby Connor– soliloquy
I just watched that scene again (I have it recorded) and that isn't exactly what she said. She simply said the following:
"My greatest fear is that one day I shall look into the face of my son and see the same dark hunger there."
While Haytham was unaware of Connor until sometime just prior to the events in Sequence 9 (per the dialogue in S9M2), I don't think that Connor's mother hid him, per se. From her monologue, it seems to imply that he had bigger things to attend to and she simply wasn't a part of that life. It sounds to me like they spent some time together, but probably no more than a few weeks or months.
1 – How Ziio knows Achilles. Was she actually trained as an Assassin? Was he her safe haven from Haytham when pregnant? Both?
I'm still not convinced that they had ever met. She wouldn't have needed safe haven, as Haytham isn't the type who would feel the need to control her and keep her close. He was way too nonchalant about all their interactions (and everything else, really) for me to believe that he is the type who would need to go looking for her again after he left to resume his Templar duties.
2 – Did Ziio know Haytham and his merry band of not-so-gentlemen were Templars before they met?
Unlikely, in my opinion. I'm sure when they were together he tried to convince her of the virtues of the Templar way, but she simply didn't share his views. That may be the very reason why he resumed his life in Boston and she resumed hers in her village.
3 – Did Ziio keep Haytham secret from baby Connor?
Given how Connor was already aware of his father, I can only assume that Connor's mother told him about his father and that she didn't share his ideals. It would make sense since he would definitely have asked about his father while growing up. I'm sure she told him everything. No reason not to, since she would want to make it clear that he wouldn't grow up to be the same man. Parents don't just sit back and hope their kids will grow into good people, they try to shape and mold them, and discourage certain types of behavior. I'm sure she told him exactly what his father was and why his ways were wrong.
Firstly, I think the Clan Mother knows more than she lets on about the Assassins and Templars. She seems to know the land must be protected. Other tribes do sell their land to the intruders, but she knows they mustn’t.
That doesn't mean that there's any influence from Juno. All of the tribes knew that the land was of utmost importance. That's the very core of their belief. But many were forced into giving up and/or selling their land by the colonists, just as Johnson was doing to Connor's tribe later in the game. She said that they are trapped between the fact that they will be forced to fight to avoid being destroyed and the knowledge that doing so also threatens to destroy them. She seemed pretty indecisive. She certainly didn't seem like she was trying to uphold some divine order instructed to her sometime in the past.
(leading partly to his severe cynicism about conquering the Templars).
I think this was mostly due to the fact that Haytham's group wiped out the rest of the colonial Assassins. It was either Lee or Hickey that mentioned this in one of the prison scenes. With only a crippled old man left in a crumbling house with no source of income, he would likely give up.
Given how he repeatedly turned Connor away (for three straight days), I don't think he was just biding his time until the son of his last student would come along, like some diving providence. No, he had given up completely and needed a lot of convincing to decide to try again.
1 – A history between Haytham and Achilles pre-AC3. Haytham didn’t come to the Americas until the beginning of the game. I think Achilles was born, or at least spent much of his life, in the colonies. Their paths likely never met before the events that transpired in AC3.
As I mentioned, Haytham's group eliminated all of the colonial Assassins. Given that Achilles is still alive, either they were never aware of him (probably already too old/too crippled to be out there fighting Haytham) or they assumed he was killed but he somehow survived without their knowledge. I'd say the former is far more likely.
I doubt that Achilles had ever met any of the men pictured in his basement. I'm sure the information came from the other Assassins before they died.
2 – I don’t think Ziio knew Haytham was a Templar until after the conception of Connor. I thought she said that she realized his ways in her soliloquy.
She only mentioned "his eyes were ever fixed upon the future – one in which his Templar brethren controlled all". She knew he was a Templar when she was with him. I'm sure he would have tried to get her to join them, so it makes sense that he explained at least the basics of Templar-hood to her. Her fear of that philosophy would have kept her from joining him. I imagine this is the very reason they didn't stay together.
Double McStab with Cheese wrote:
1 – Ziio knows Achilles – as per Clan Mother speech – “... he will help you as he helped your mother.”I never got that at all, after two playthroughs of the game. I'll have to go back and watch that scene again, but I don't recall it mentioning any connection between Connor's mother and Achilles.
http://www.youtube.com/watch?feature=player_embedded&v=TeF_ntFVjqs&t=7m40s
It's at 7:45 or so... "It was borne by a man who will surely help you, as he once helped your mother."
It was the most powerful thing that I took from that scene on my playthrough... not the protecting of the land, or fighting for what's right... but the familial connection already to the Assassins pre-Connor.
“Force has no place where there is need of skill." Herodotus
Also, you may want to put some of your response in spoilers as the person who started this thread has only finished sequence 5. 
“Force has no place where there is need of skill." Herodotus
Also, you may want to put some of your response in spoilers as the person who started this thread has only finished sequence 5.
There wasn't really anything spoiled, so no worries.
“Force has no place where there is need of skill." Herodotus
Double McStab with Cheese wrote:
Also, you may want to put some of your response in spoilers as the person who started this thread has only finished sequence 5.There wasn't really anything spoiled, so no worries.
You're good. I assumed there would be some closure to the Haytham/Connor relationship, but it's not a huge deal knowing where it comes in the memory sequences. Presumably it flows with the story itself and will be anticipated by me when it's time anyway.
Unfortunately I don't have much free time on my hands and will probably go about 5 weeks in between finishing Sequence 5 and beginning Sequence 6. I'm sure I'll beat the game at some point.
Double McStab with Cheese wrote:
Firstly, I think the Clan Mother knows more than she lets on about the Assassins and Templars. She seems to know the land must be protected. Other tribes do sell their land to the intruders, but she knows they mustn’t.That doesn't mean that there's any influence from Juno. All of the tribes knew that the land was of utmost importance. That's the very core of their belief. But many were forced into giving up and/or selling their land by the colonists, just as Johnson was doing to Connor's tribe later in the game. She said that they are trapped between the fact that they will be forced to fight to avoid being destroyed and the knowledge that doing so also threatens to destroy them. She seemed pretty indecisive. She certainly didn't seem like she was trying to uphold some divine order instructed to her sometime in the past.
Was doing some light reading tonight.
Here's info straight from the source (Ubisoft) on the matter of Connor's Tribe knowing more than they let on / being involved with Assassins:
American Revolution
The Assassins recognized the importance of the Americas long before the Templars, and in the early sixteenth century, they sent men to establish the Brotherhood and secure peace.As the Assassins traded and shared ideas with the indigenous populations, they discovered the Native's close link to the First Civilization. In particular, one village of the Kanien'kehá:ka tribe held a mysterious structure in very high regard in their religious iconography. The Assassins slowly gained the village's trust and the residents eventually allowed their new allies access to their sacred structure.
The Assassins were shocked to find an ancient temple built by the First Civilization. Unclear as to its purpose but certain of its importance the Assassins devoted themselves to the mysterious group, vowing to protect their people, culture and territory at all costs.
It does provide some background to the Assassins and Connor's tribe before the events of the Seven Years War at the beginning of AC3. It does also say that after the Seven Years War the Assassin's ranks were decimated with the only known survivor going into hiding... which we know.
It doesn't say if the tribe was cognizant of the Assassins, though. Just that the Assassins were devoted to the tribe. I surmise that it would be to mutual benefit for both sides to be on board.
"We're an organization fighting oppression and want to help your tribe."
"Okay."
"We will protect you as best we can from the Templars. We are Assassins."
"Glad to have your help, whatever your motives."
“Force has no place where there is need of skill." Herodotus
I was initially surprised by that scene but i shrugged it off as "his mother told him about Haytham". If it was Achilles who told Connor everything about his father then i don't know why they wouldn't include that in the long expositional cutscene.
Exactly. That's not the kind of sudden revelation you just gloss over. It makes much more sense that he learned while growing up.