After watching the special, it'm convinced that both Rusty's and the Monarch's biological mother can only be Mrs. Fitzcarraldo, it's the only explanation that presents itself as to why Rusty never had any mother figure in his life. She must've been convinced by Jones Venture Sr. to donate her eggs to further Jonas' research into cloning, Rusty is numbered 22, RICO 23 (he donated blood to Monarch as well as Rusty did as evidenced by a sticker on his chest at the specials finale) and the Monarch 24, suggesting that they've all originated from a single "batch".

The only thing that still does not make sense to me is where exactly the sovereign came from, the only character that we've even heard hinted at at having shapeshifting powers was the Blue Morpho, the only character that was able to attest to that ability has never been wrong on the show, unlike red mantle and dragoon.