As a suggestion, perhaps you might want to elaborate on a lesser known character in the story. If you plan to do all this. It could work, but what you'll need to do is show that character development that happened in the middle. Between the 18 years of stuff. A lot of things will have had to have happened to lead many of these characters to such extreme desperate measures. I also disagree with what you've suggested as happening. But, if I knew what led them to such measures, maybe I would.

Cyan becoming the leader of a new Doma is VERY likely. In fact, I wouldn't have been surprised if that was in the real ending. I might remind some people, that Sabin and Edgar weren't (although they were shown this way) that close. I mean hey, Sabin and Edgar hadn't seen each other for years. I'm sure they could (provided there was an extremely good manipulator) turn on each other. The game would HAVE to show how this happens. And it would have to show it slowly and logically so that people could grasp it. It's not WHAT happens that's important in a story, it's how it happens. It's just got to be consistent with their specific character flaws. And although these things are plausible, they're not consistent with the characters we know. Over the years, this could change, but you would have to show that.