Here's a look at some of the most memorable controversies over the last two decades under Belichick.
BELICHICK'S MESSY ARRIVAL IN NEW ENGLAND
The news conference to introduce Belichick as the new head coach turned out to be quite the opposite. Belichick scribbled his resignation on a piece of paper: "I resign as HC of the NYJ." Belichick then delivered a resignation announcement.
The Jets demanded compensation from the Patriots because Belichick was still under contract with the team. The NFL stepped in and the Jets were awarded the Patriots' first-round draft pick in 2000. This was also the opening salvo in a heated Jets-Patriots rivalry that continues to this day.
Perhaps the most publicized scandal involving the Patriots took place on Sept. 9, 2007 when the team was caught illegally videotaping Jets' coaches' defensive signals. And thus the term "spy-gate" was introduced to the sports world.
Belichick later acknowledged that he violated NFL rules prohibiting filming opponents' signals but insisted there was no intent to hide what he was doing.
"I made a mistake," Belichick said in a televised interview. "I was wrong. I was wrong."
TUCK RULE GAME
Even 13 years after the infamous "tuck rule" game, critics still believe it's a game the Patriots should have never won.
That was until referees overturned the play, saying Brady's arm was moving forward, thus making it an incomplete pass and not a fumble. The refs pointed to the "tuck rule," which was eliminated from the NFL rulebook in 2013.
The rest, as they say, is history. Patriots went on to win the game and eventually their first Super Bowl.
A week before deflate-gate became a household name, there was some controversy swirling around the Patriots' playoff win over the Baltimore Ravens in a tightly contested 35-31 game. Ravens coach John Harbaugh accused the Pats of a "substitution trick" that was "clearly deception."
The Patriots dug into their bag of tricks on their second drive of the third quarter, lining up just four offensive linemen and declaring a normally eligible receiver as ineligible to keep Baltimore off balance. Ravens players were confused about which Patriots to match up with in coverage.
Harbaugh said it was a tactic that "nobody has ever seen before."
Brady wanted none of that and fired back after the game.
"Maybe those guys gotta study the rulebook and figure it out. We obviously knew what we were doing and we made some pretty important plays. It was a real good weapon for us," he said.
According to ESPN, 11 of the 12 balls used by the team were under-inflated by two pounds per square inch. Footballs, which are weighed before the game, must be inflated to no less than 12.5 pounds per square inch.
A deflated ball could be easier for the quarterback to grip in bad weather, such as in Sunday's rain at Gillette Stadium in Foxborough, Massachusetts.
The NFL is investigating and Belichick said this earlier this week that his team will cooperate with the NFL's investigation.
"We'll cooperate fully with whatever the league wants us, whatever questions they ask us," Belichick said.