I imagine Sephiroth will try to have the situation in his own way, on his own to begin with, but when things start to slip out of his advantage he's certainly dirty enough to 'use' the contagion he's planted in Terra and Vlad. Jenova cells, depending on how well they have bonded with a recipients DNA are literally like a mind/body-controlling cancer.

How about using a Vlad-clone to appear to have turned on the other heroes, while the real!Vlad takes cover and waits for an opportunity? Perhaps Tazendra's urging will go some way to resist the pull to submit to Sephiroth's will?

I like the idea of him coming in at the end and stabbing him in the back when Sephiroth thinks he's won because this is a recurring thing in canon as well. So if we get to a stage when everyone else is dead? Could well happen.