From 2000 until 2016, the Bills would fail to make the playoffs, a streak that would end in 2017. After the 2000 season ended, general manager John Butler left the team to take the same position with the San Diego Chargers.
Doug Flutie led the Bills to a 10–5 record in 1999 but, in a controversial decision, was replaced by Rob Johnson for the playoffs by coach Wade Phillips, who later said he had permission from Bills owner Ralph Wilson to do so. The Bills lost 22–16 to the eventual AFC champion Tennessee Titans in a game that has become known as the Music City Miracle, where the Titans scored on the penultimate play of the game—a kickoff return following the Bills' apparent game-clinching field goal. After the season ended, Flutie was named the Bills' backup and only played late in games or when Johnson was injured; the two split playing time in seven games. Despite getting his chances in December to help the team, Flutie was unable to get the team key wins in December, sealing his fate as a casualty to a roster cut. Flutie would be released at the end of the 2000 season and Johnson would spend an injury-plagued 2001 season with the Bills before also being released.
Phillips was fired shortly after the season by Wilson, citing Phillips' refusal to fire special teams coach Ronnie Jones. (Football statistics site Football Outsiders calculates that the 2000 Bills had the worst special teams unit of any single-season team from 1993–2010.) Said Wilson at the time, ""Buffalo special teams’ record was among the worst in the National Football League last season. ... I felt we needed a change and that my request was reasonable... I did not want to release Wade, but his refusal left me with no option." Said Football Outsiders of Buffalo's special teams in 2000, "Could special teams possibly be that negative? Oh, yes. They could. The 2000 Buffalo Bills had the worst special teams of any team in any season for which data. I would not be shocked if they had the worst special teams of all time, except maybe for some expansion teams in the sixties and seventies. Everything about special teams was horrible for the Bills that year, but Steve Christie was the biggest black hole among a galaxy of sucking black holes. ...Christie's average kickoff went only 55.6 yards, 7.5 yards less than the league average. And the bad kickoffs didn't just come late in the season in Buffalo's usual snow and wind. ...On the season, 18 of his kickoffs went for 50 yards or less. No other kicker had more than 10 kicks that short. ...Buffalo allowed opponents kick returns worth 22 points more than the league average. ...So the average opposing drive after a Buffalo kickoff started at the 37-yard line. Wow." Buffalo hired Tom Donahoe to become the new general manager the following season. Donahoe hired Tennessee Titans defensive coordinator Gregg Williams to be the head coach in a season which saw the rebuilding team struggle to a 3–13 record.