In a 457-page transcript released Tuesday, Brady maintained his innocence in the Deflategate scandal. He denied discussing air-pressure levels with the ball boys or even thinking about how inflated the footballs were when he selected them. He said he was not aware of the rules that govern the inflation levels of footballs until after an Oct. 16, 2014, game against the New York Jets in which he complained about the size of the footballs.
Brady also said he never asked anyone from the Patriots to tamper with footballs.
Brady was suspended four games and the team was docked $1 million and two draft picks after an NFL-sanctioned investigation by Wells found the Patriots supplied improperly inflated footballs for the conference championship game against the Indianapolis Colts, which New England won 45-7.
Brady appealed the punishment. Goodell decided to hear the appeal himself and upheld the penalty. Both sides went to federal court, and U.S. District Judge Richard Berman told the sides to work out a settlement. To encourage them, he ordered both Brady and Goodell to appear in court in person during the NFL preseason.
The transcript filed by the NFL Players Association on Tuesday in Manhattan federal court included the appeal testimony from Brady and Wells on June 23. Wells explained that he did not believe Brady had nothing to do with the ball deflation because Brady refused to provide all of the documents that were requested.
"In my almost 40 years of practice, I think that was one of the most ill-advised decisions I have ever seen, because it hurt how I viewed his credibility," Wells testified. "It hurt my assessment of his credibility for him to begin his interview by telling me he declined to give me the documents."
Wells' investigation found text messages between Brady and a pair of equipment managers -- one of whom referred to himself as "the Deflator" -- discussing the preparation of footballs for the Jan. 18 game. The Patriots advanced to the Super Bowl and beat the Seattle Seahawks 28-24 for Brady's fourth NFL title.
Although Wells asked repeatedly for Brady's cellphone, the investigator also testified: "I did not tell Mr. Brady at any time that he would be subject to punishment for not giving -- not turning over the documents. I did not say anything like that."
Brady's attorneys did provide copies of his emails to investigators.
His lawyers have said the league made up its rules without proper notice to Brady and that it didn't follow its rules at all in some cases. They also have questioned whether Goodell was independent enough to conduct a fair hearing, even though the collective bargaining agreement gives him that authority.
The NFLPA called four witnesses at the appeal hearing: Brady, Wells, NFL executive vice president Troy Vincent and Ted Snyder, dean of the Yale School of Management. The NFL Management Council called Dr. Robert Caligiuri and Duane L. Steffey of Exponent, the group that conducted tests on footballs as part of the Wells investigation, as well as Daniel Marlow, a professor of statistics at Princeton.
Tuesday's filing also included exhibits, one of which was an email from the Colts' equipment manager to general manager Ryan Grigson that said the Ravens had warned the Colts about issues with the footballs after Baltimore lost to the Patriots in an AFC divisional playoff game. The email from Sean Sullivan said coach Chuck Pagano, who previously was an assistant and defensive coordinator for the Ravens, was alerted by Baltimore special teams coordinator Jerry Rosburg.
The Ravens have long denied that they warned the Colts about the underinflated footballs.
ESPN.com's Mike Reiss and The Associated Press contributed to this report.
Schefter: Brady testimony forceful
Adam Schefter discusses Patriots QB Tom Brady's Deflategate testimony, in which he denied under oath that he tampered with footballs before the AFC title game.
Brady's testimony released
Field Yates discusses the ramifications of the release of the transcript from Patriots QB Tom Brady's June testimony in the Deflategate hearing.