That might be the case, but I'm still hoping Yuuji hasn't been subjugated in the first place. We don't really know what the other entities inside him want. As long as we are talking about the tomogara, for example, they are villains, so logically they should be just as eager to annihilate each other as anybody other, so their real ambitions and plans could be swinging in any direction. Yuuji might have accepted a costly compromise to reach his own goals, assuming he came up with one during the void scene of the first ep.

The thirteen in a dozen plot element of Yuuji being now asleep and waking up when Shana is in danger would really create a miserable ending for this series. I'd rather see something like Yuuji sacrificing himself to put an end to Bal Masque, leaving Shana live with a conflicting memory of him.