Ah. That makes sense actually. Time was reversed and Ex-Keine created a new history where Reimu seals Flan before she can kill Remi.

So that's how things turned out different, even though Sakuya passed out before she could change anything, and then seemed like she didn't remember what originally happened (though she senses something odd in the re-written time).

Keine used her Ex-power to change history.

But who would be lord of Gensou City if not Yukari? Surely not Keine? Is the schoolteacher working directly for the Dragon?

Red_Inugami said:
But who would be lord of Gensou City if not Yukari? Surely not Keine? Is the schoolteacher working directly for the Dragon?

She might be, but I suspect Yukari is refering to a natural phenomena type deal, something like a Mother Earth, that Keine is an agent for. Like being an agent for law or chaos or balance.

...Am I the only one who thinks EX-Keine's silhouette looks rather manly?

i think is zun who control both genso city and gensokyo and keine/ex is just his assistant