Tom Brady will sit out the first four games of the 2015 season for his role in the Deflategate scandal after having his suspension upheld on Tuesday.

The New England Patriots quarterback had appealed the initial ruling in a hearing heard by Roger Goodell, but the commissioner found enough evidence to keep the suspension at four games.

Troy Vincent, the league's executive vice-president of football operations, handed down the initial suspension to three-time Super Bowl MVP for his role in deflating footballs during last year’s AFC Championship game against the Indianapolis Colts, which the Patriots won 45-7.

Vincent also fined the Patriots $1 million and stripped them of a first-round draft pick next year and a fourth-rounder in 2017. Those penalties will also stand after the Patriots elected not to appeal them.

The defending Super Bowl champions will open their season against the Pittsburgh Steelers in Week 1 followed by the facing Buffalo Bills, Jacksonville Jaguars, and finally the Dallas Cowboys in Week 5 after their Week 4 bye. He is eligible to return in Week 6 against the Indianapolis Colts.

The suspension is set to cost Brady close to $2 million in game checks.

The NFLPA, on behalf of Brady, will now pursue legal action against the NFL to have his suspension vacated. In a legal case, Brady could receive an injunction to play until the case is resolved. ESPN's Jim Trotter reports Brady approved to NFLPA to file a lawsuit within hours of Goodell's ruling.

Scott Soshnick of Bloomberg repports the NFL has asked the federal court to confirm their suspension of Brady with a complaint filed in Manhattan. 

The commissioner pointed to Brady's destroyed cellphone as further evidence in his role.

"On or shortly before March 6, the day that Tom Brady met with independent investigator Ted Wells and his colleagues, Brady directed that the cell phone he had used for the prior four months be destroyed," the NFL's statement read. "He did so even though he was aware that the investigators had requested access to text messages and other electronic information that had been stored on that phone. ‎During the four months that the cell phone was in use, Brady had exchanged nearly 10,000 text messages, none of which can now be retrieved from that device. The destruction of the cell phone was not disclosed until June 18, almost four months after the investigators had first sought electronic information from Brady."

"The commissioner found that Brady’s deliberate destruction of potentially relevant evidence went beyond a mere failure to cooperate in the investigation and supported a finding that he had sought to hide evidence of his own participation in the underlying scheme to alter the footballs," the statement concluded.

The NFL player's association said the NFL received all phone records requested from Brady.

"The fact that the NFL would resort to basing a suspension on a smoke screen of irrelevant text messages instead of admitting that they have all of the phone records they asked for is a new low, even for them, but it does nothing to correct their errors," the NFLPA statement read. "The NFLPA will appeal this outrageous decision on behalf of Tom Brady."

Brady's agent, Don Yee, released a statement following the decision, calling the NFL's appeal process sham.

"The Commissioner’s decision is deeply disappointing, but not surprising because the appeal process was thoroughly lacking in procedural fairness," said Yee. "Most importantly, neither Tom nor the Patriots did anything wrong. And the NFL has no evidence that anything inappropriate occurred."

"Tom was completely transparent. All of the electronic information was ignored; we don’t know why," Yee added. "The extent to which Tom opened up his private life to the Commissioner will become clear in the coming days."

Behind Brady, the Patriots have 2014 second-round pick Jimmy Garoppolo and veteran Matt Flynn at quarterback. Garoppolo passed for 182 yards with a completion rate of 70.4 per cent for one touchdown and three interceptions across three appearances with the Patriots last season. Flynn owns a 3-4 record as a starter in his career. In 2013, he started four games for the Green Bay Packers, passing for 1,146 yards with seven touchdowns and four interceptions.

Brady has started every game for the Patriots since returning from a torn ACL in the 2009 season.

The Patriots report for camp on Wednesday, with their first practice taking place one day later.

The team released the following statement on Tuesday:

“We are extremely disappointed in today’s ruling by Commissioner Goodell,” the team statement read. “We cannot comprehend the league’s position in this matter. Most would agree that the penalties levied originally were excessive and unprecedented, especially in light of the fact that the league has no hard evidence of wrongdoing. We continue to unequivocally believe in and support Tom Brady. We also believe that the laws of science continue to underscore the folly of this entire ordeal."

Given all of this, it is incomprehensible as to why the league is attempting to destroy the reputation of one of its greatest players and representatives.”