Is there a sort of kinship with Nagini being the last of her kind and Rhaegar establishing himself as the last of both the Gaunt and Riddle bloodlines?
rhaegar has made peace with him being the last riddle ( and gaunt in an au where ominis doesn't exist ofc ) , the bloodline coming to a stagnant with him lasting eternal. the lack of family bore a deep hole in his heart back at wool's, it was filled by nagini, and later on ominis, rhaegar would do anything for his chosen family. ( the rest of the gaunts can choke on a pickle ) and the heir would have as little guilt about killing the rest of the gaunts as he had framing his uncle for mass murder. he refrains from acting on these thoughts, however, knowing ominis wouldn't condone it.
it's different for nagini, it was way more painful for her. early on in his hogwarts years did rhaegar find out that the albanian crownheads were declared extinct a good century ago. impossible, of course, nagini was right there! and if she was alive, who was to say there weren't other surviving members scattered about. nagini was in deep denial. rhaegar promised her the first country they'd visit after his graduation was albania, they'd search far and wide in her ancestral homeland for any other members of her family, nagini even went on her own during his stay at wool's during the summer. ( a foolish and risky move, but she did not care )
naturally nothing came of it. they travelled and searched, found only confirmation of what the dragonology professors claimed. rhaegar then scoured the black markets, he found only the remains of nagini's mother. and three eggs that never hatched. the mother was picked apart and sold, rhaegar saved off her what he could, he demanded the three eggs, as well. ( and who'd refuse a demand of the head of the sacred twenty-eight ) nagini's mother , what remained of her, was laid to rest in albania, the eggs are kept in rhaegar's home.
it broke nagini's heart, of course, but at least the winged mountain had closure. and she still had rhaegar. albanian crownheads would mate and lay for life, spending their centuries with one partner only. rhaegar, in a way, fulfilled this purpose. they're together, like it's always been. and they'd stay together eternally. it's a duality, in a way, bound by soul and spirit. but ominis, too, is welcome in their merry band. all three of them knowing what it's like to be alone.
rhaegar almost knows, he has ominis.
ominis knows figuratively, the gaunts abandoned him.
nagini kows literally, she is the last.
at least ominis can continue the gaunt bloodlone, assuming he wishes for it, ominis is the only one worthy to do so, he is the only gaunt that does good - who can produce good. his brother's potential children would CERTAINLY inherit their father's morals and benevolent will. this expectation means a lot of preassure, of course, so rhaegar never voices these thoughts to his brother, but should ominis express a desire for children, should he have children, uncle rhaegar gaunt would be their eternal guardian. and should the bloodline grow rotten again, return to it's abyssal roots, rhaegar, too, would act as their judge and executioner.
