Wow, such a heated debate...
Ok look, in cut material that TSLRP is restoring Bao-Dur mentions returning to Malachor to activate the Generator again. Then after you deal with the Atris problem, Grenn notices Bao-dur is gone. And in another cut line, Bao-Dur asks the remote to "Make my Sacrifice matter".
And so based upon those three things* it is easy to assume he followed Kreia to Malachor while you were on Telos, tried to activate the generator, but was killed. And even if this isn't EXACTLY** what OE intended, every other party member has a end-game resolution; Mira, Hanharr, Atton, Brianna, Mical, HK-47, Remote, Go-To, Visas Marr, and Kreia. And like Bao-dur every ones ending was cut or trimmed down to a shell of what it could have been.
So don't come complaining that this is BS, it makes perfect sense if you look at Bao-dur's character. He thought he could keep Czerka from messing up Telos on his own, he thought he could stop the Republic's enemies with his OWN creations, AND he very much regrets having made the generator in the first place.
There enjoy my argument.
*There are more but not worth mentioning here.
**Not everything in TSLRP, M4-78RP, or TSLCR is EXACTLY like Obsidian Intended.