The Templars have captured that pesky Assassin that always gets in their way and messes with their plans, and Haytham, being severely annoyed, decides to deal with him personally. He sets about breaking Connor in every way he can - noncon, torture, brain-washing, until the young man is completely dependent on him. And then and only then does Haytham find out somehow that this young man he abused and broke and made his (fuck)toy is his son.