The four-game suspension of New England Patriots quarterback Tom Brady for his alleged role in the Deflate-gate scandal has been upheld, the NFL announced Tuesday, a move that will bring about a high-profile legal battle between the Super Bowl winner and the league.

Brady was punished in May after a league-led investigation determined that he was “generally aware” of a plot to take air out of footballs before this year’s AFC Championship Game, which is believed to make them easier to catch, and is a violation of NFL rules.

According to the NFL decision released Tuesday, the suspension is being upheld in part because Brady directed that a cell phone, which contained four months worth of text messages that would have been vital to their investigation, be destroyed prior to his first contact with attorney Ted Wells, who was leading the league’s investigation. The NFL says that it was not notified about the destruction of the cell phone until June 18, nearly four months after the data was requested. The league found that Brady exchanged nearly 10,000 texts during the period in question, none of which can now be retrieved.

RELATED: Why Roger Goodell was always doomed on ‘Deflate-gate’

“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 NFL said in a statement. Brady had told the NFL that he regularly has old phones destroyed by an assistant when he gets a new one (“So that no one can ever, you know, reset it or do something where the information is available to anyone.”), but, according to the league, he provided no explanation for why he destroyed the 4-month-old phone in question just prior to his meeting with Wells.

The Patriots star has steadfastly denied any knowledge of or involvement in the deflating of footballs and testified in person for several hours at an appeal hearing of the NFL’s decision in June. In the weeks since, it has been widely speculated that the NFL and Brady would reach some sort of compromise – a reduction in his suspension, perhaps – in the hopes of avoiding a prolonged legal fight over the ruling.

Everyone please pray for Tom Brady as he will have to stay in this prison during his suspension pic.twitter.com/1GCtPKi2eh — Will Ferrell (@Will___Ferrell) July 28, 2015

However, with Tuesday’s decision, embattled NFL Commissioner Roger Goodell doubled down on the findings of Wells, whose report cast a shadow over Brady’s legacy. Goodell, who has been criticized in the past for enjoying a close personal relationship with Patriots owner Robert Kraft, said Brady “engaged in conduct detrimental to the integrity of, and public confidence in, the game of professional football.”

NBC News has confirmed that the NFL Players Association will appeal the latest decision from the league in federal court on behalf of Brady. The NFLPA called the NFL’s decision to uphold the suspension “outrageous” in a statement released Tuesday and claimed that it was based on a “smoke screen of irrelevant text messages.”

“The Commissioner’s decision is deeply disappointing, but not surprising because the appeal process was thoroughly lacking in procedural fairness,” Brady’s agent and attorney Don Yee said in a separate statement.

“Most importantly, neither Tom nor the Patriots did anything wrong. And the NFL has no evidence that anything inappropriate occurred,” Yee added. Brady’s rep went to on to call the appeals process a “sham” and the Wells report’s science “junk.”

In addition to suspending Brady for four games, the Patriots were fined $1 million and stripped of two future draft picks by the league for their alleged involvement in the scandal. The team did not appeal the league’s decision at the time.

However, on Tuesday the team came to Brady’s defense. “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,” they said in a statement. They added: “We continue to unequivocally believe in and support Tom Brady.”

