Prediction:
He's shit now, and his spirit power is shit, so the flower is wilted, right? He doesn't have plot armor and bonuses anymore, so he won't become strong like he is supposed to, which would have restored his flower.
Therefore, she must train him so he can grow stronger, like fattening up a pig for slaughter. Train him -> Grow his spirit power -> Lead him to nad ending -> Take his flower.
However, during the course of this, she'll grow closer to him, because he's pretty endearing now that he's different.
They'll fall for each other, and then it turns out that by being together, as one, it replicates the effects of having a whole crimson flower heart enough to keep them both alive. The end.
At some point during all this, there will be some complications with the player manipulating stuff and maybe the game trying to keep things on track. Or some of his memories will return. Some kind of drama.
And there you have it.