First off: The Discipline Fortitude can't be bypassed. At least not that I know of. It's the only way for a vampire to soak aggravated damage, and not even a reliable one. So the only way to outright kill him, is to throw punches at him. Take Path of Blood 5 and burn his blood.
Another way would be to let him burn his own blood until he is in frenzy. He won't have that much Blood left to boost his physical traits or use Celerity or other Disciplines. It's way too risky I'd say, but it is a way to deal with him.
But for goodness sake you're playing a Tremere not a Brujah or Gangrel. You're taking the wrong approach to this problem. You're a social clan, so to speak. You have a tight-knit clan and you should have friends. You can ask your superiors to teach you a new Ritual. (Sorry that I can't tell you which one to pick, I don't know them all)
A sixth generation vampire may be immune to your Dominate but if you have a Toreador or Ventrue with you he isn't immune to their Presence. That might cost you some favours but can help you defeating him.
Another possibility is to let him make a fool of himself in front of the whole domain. It sure as hell will make your unlife way more difficult but when done correctly you not only have a hell of character play, be much more satisfied with yourself, but also you'll get some new Allies. You'll get some new Enemies, of course, but did you want to play a vampire without having enemies?
My best advice for you is to not take this enemy head on. If you want to destroy him do it slowly and with a Masterplan. Of course that is difficult but it's the best way to deal with such an enemy. If it's a Gangrel you just can't take him head on. He'll kill you within the first two seconds of the fight. If it's a Ventrue or Ravnos (all assuming he has Fortitude as clan discipline) then it's going to just take two minutes to kill your vampire.
So "just" take it slowly and (for instance) find (or create) some evidences that he wanted to overthrow the Prince (or if he's the Prince that he wanted to disband the Primogen Council) and perhaps he's got a Blood Hunt waiting for him.
If for any reason all your plans are being thwarted and he's still on top, you should perhaps talk to your DM about that particular character of his.