As the season progressed, however, both teams would end up in very different places. Buffalo's high-powered offense from 2002 was unable to reprise as the Bills and QB Drew Bledsoe struggled all season long. In fact, they went an entire month without scoring a TD on offense. All of this culminated in a 6-10 record; not quite enough for a playoff berth. The Patriots, on the other hand, did not miss Milloy after their loss on week 1. After the loss to Washington in fourth game of the season, they would embark on a 21-game winning streak that spanned two seasons. With 12 consecutive regular season victories to close out 2003 at 14-2 (including a 31-0 shutout at home of their own against the Buffalo Bills in week 17), the Patriots defeated the Tennessee Titans 17-14 in the AFC Divisional Playoffs, the Indianapolis Colts 24-14 in the AFC Championship and the Carolina Panthers 32-29 in Super Bowl XXXVIII. The Patriots opened the 2004 season 6-0 before finally losing to the Pittsburgh Steelers on Halloween. That season, New England was able to win its third championship in four seasons with a 24-21 victory over the Philadelphia Eagles in Super Bowl XXXIX.

While Milloy had enjoyed some success in Buffalo, many question why he was unwilling to renegotiate his contract when approached by the Patriots. Although Milloy helped the Bills to a six-game win streak late in the 2004 campaign (to erase an 0-4 start), they have not made the playoffs in his three seasons there. With the uncertainty surrounding the Bills front office, personnel, and, perhaps coaching staff this coming offseason, one must wonder if Milloy will even be back for a fourth. The Patriots, on the other hand, have been considered a modern-day dynasty in an era of the salary cap that was designed to promote parity. They have won three Super Bowls in four years; all while emphasizing a team-first concept. The Patriots continue to compete at a high level despite many injury problems and, even though they failed to win an NFL-record third consecutive title, they are expected to contend for years to come. In fact, following the Patriots victory over the Eagles in Super Bowl XXXIX, Milloy criticized the Patriots organization for refusing to pay players what they are worth on the open market. In addition, he criticized the players for not testing the open market as those who have played on the most recent Super Bowl championship team are more likely to command higher salaries. He was infamously quoted as "you can't feed your family off of Super Bowl rings", which has caused many Patriot fans to lose a lot of respect for their one-time defensive captain. The context of the quote is almost laughable considering even a rookie NFL player makes well more than the average family.

Milloy, a four-time Pro-Bowler, was released by the Bills on Wednesday, March 1, 2006 in a salary cap related move.

On March 17, 2006, Milloy was signed to a three-year, $6 million dollar contract by the Atlanta Falcons.