From what I recall, he had all kinds of legal problems and the 49ers were in major cap hell/turmoil and basically collapsed during the '99 season. The 49ers had been a dominant NFL force since the 1981 season and between the cap turmoil and DeBartolo's legal and financial problems, he was allowed to hand over the keys to his sister.

The 49ers fell hard really fast that year and it took many years for that team to recovery. They had an aging, expensive roster and basically had to purge most of it. With Steve Young's season-ending injury occurring early in the season, the team quickly collapsed after one of the most dominant runs in NFL history.

I am sure 49ers fans can explain it better but from what I recall Eddie had become disgraced and the league wanted to quickly get him out of the picture to protect San Francisco's brand.