He was worn out. For around 6-7 years, Ware played the most snaps in football. You really gotta think this out before falling for the media spew.
Parcells was asked that in a pc and while he didn't just come out and say it, anytime Ware was out the other team rolled. They had a coach on Ware watch.
The problem with Ware and Ratliff was they were gassed by the 4Q as they were both high motor guys. Johnson had the luxury of resting his DL and OL for the 4Q so that they'd be fresh.
The other thing is that the NFL was far more balanced run to pass when Ware played so fighting off OL in the run game takes a lot out of DL, which is why they try and keep them off the LB's.