Mulkey got told "You'd better take that LSU job, cause we're not putting up with your shit, anymore." It all came down to the new basketball arena. Mulkey wanted it on campus, in between the Ferrell Center and the baseball and softball stadiums. Baylor was in negotiations with City of Waco and some private developers to put it on the bank of the Brazos, on the downtown side of I-35. The arena project will cost $185 million. Waco's chipping in $65 million, and it's going to anchor a $700 million downtown river development.
They told Mulkey several times to STFU, they were going to put a statue of her up in front of the new arena, and make everything look smooth on the outside. She wouldn't shut up. Completing the negotiations required meet and greets with a lot of people with serious money, and Baylor was tired of Mulkey showing her ass at every possible moment, and they weren't going to let her go into negotiation meetings screaming about having the arena in an area that was too small and was going to remove about 50% of the parking from the three other facilities there.
She'd been a pain in the ass for years, and you can usually get away with being an ass when you're winning, BUT when the money boys tell you to sit down and STFU, you either do it or go someplace else.
Both sides have been quiet about it, but it wasn't Mulkey's choice.
The only coach who's voluntarily left Baylor since I started covering them in around 2006* is Matt Rhule, and he was writing his number on NFL bathroom stalls before he got the Baylor job.
*Disclaimer: I don't cover anything except football, basketball and women's basketball, and I cover as little women's basketball as I have to.