Let's review Merlin and Nynian's relationship.
Merlin-
A young woman who adopted the role of being a man to the point of identifying as a man. Someone who has spent her entire life fighting a war that she knew would end in her death. She was given a reprieve under Commodore Pei and chose to sacrifice her life. Even though Merlin did not remember making that choice, it was a choice his personality matrix could easily have made. Since waking on Safehold, Merlin has spent his time fighting a clandestine war for the lives of people most of whom who would hate him if they new what he truly was. She grew up avoiding intimacy and he lived on Safehold guarding the secret of his identity, the secret of what he is. those that knew his secret were friends but almost all were unsuitable for intimacy. Finding someone that was suitable and would be honestly attracted to that truth would appear to him as impossible.
Nynian-
A woman who was rejected by her parents but embraced by a sisterhood of clandestine radicals sworn to honor a larger than life male ubermensch. She spent her life in the organization playing the role of a courtesan.....well being a courtesan. That is playing a role that involved real and feigned intimacy that always hid away big pieces of herself. The only people she truly trusted and could be as open as she could have been was with the women of her sisterhood. She states that she was a sensuous person and that attribute was directed at men. Yet, she could be open only to women.
Is it any that when she finds out that there truly still are larger than life ubermensch, she will be attracted to him? Any wonder that when she realizes the ubermensch is even larger than her imagination she is further intrigued? Finally, is it surprising that the ubermensch who is as male as anyone she has ever been intimate with is actually a woman with a woman's memory and instinct will draw her sense of attraction like a black hole?
Seriously here, this pair was made for each other.
