The investigative team employed scientific advisers, including a Princeton physics professor. They determined that the change in PSI (pounds per square inch) measurement in 11 of the Patriots' 24 game balls from their pregame reading to their halftime reading "cannot be explained by basic scientific principles.” Specifically, at the start of the game, each ball was inflated to 12.5 PSI, the league-mandated minimum. At halftime, two different measurements were taken. One gauge measured the balls between 10.5 and 11.85 PSI, and the other measured between 10.9 and 12.3 PSI. The report says “for the reasons described in this Report, and after a comprehensive investigation, we have concluded that, in connection with the AFC Championship Game, it is more probable than not that New England Patriots personnel participated in violations of the Playing Rules and were involved in a deliberate effort to circumvent the rules.”

The report concludes that "it is more probable than not" that full-time team employee John Jastremski, who has been a team equipment assistant for over 14 years, and Jim McNally, a part-time employee who is the officials' locker room attendant for Patriot home games, intentionally deflated game balls after they were inspected by a referee. It also was "more probable than not" that Patriots quarterback Tom Brady "was at least generally aware" of Jastremski and McNally's activities. The report also concludes that team owner Robert Kraft, head coach Bill Belichick, and head equipment manager Dave Schoenfeld did not have knowledge of any wrongdoing or participate in any wrongdoing.

Each team provides anywhere from 12 to 24 footballs to be used during the game, depending on the weather. The footballs are given to the officials 2 hours and 15 minutes prior to game time, at which point they are tested with an air gauge, and if they are from 12.5 to 13.5 PSI, the referee puts a special marking on the football and approves it for game use. The footballs then remain in the officials’ locker room, under the supervision of a locker room attendant (in this case McNally), who brings the footballs out to the field 10 minutes before kickoff. The NFL has stated that referee Walt Anderson properly inspected all 48 footballs before the game – 24 each from the Patriots and Colts.

There is no hard evidence linking Brady to Jastremski and McNally in regards to the deliberate deflation of balls, it is all circumstantial. It includes texts between Jastremski and McNally that mention Brady and his signing memorabilia for McNally, as well as several calls between Jastremski and Brady that began on Jan. 19, the day after the AFC Championship game. Yet, according to Jastremski's phone, there were no calls or texts between Jastremski and Brady for six months before the first call on Jan. 19.

McNally told referee Walt Anderson during pregame inspection that Brady wanted the Patriots’ footballs inflated to 12.5 PSI. The Colts’ preference was 13.0. Two of the Patriots’ footballs measured below the league minimum during pregame inspection and had to be inflated to 12.5. No changes were made to the Colts’ footballs. Brady, who voluntarily spoke with investigators, denied any involvement and denied even knowing McNally’s name, his job title, or his pregame responsibilities. Jastremski disputed that, saying Brady in fact knew McNally and his role. Jastremski’s phone records and text messages show that Brady spoke with Jastremski by phone six times in the three days following the AFC Championship after the two had not communicated for six months. The calls totaled about 55 minutes. Brady also checked in on him via text, “seemingly designed to calm Jastremski,” according to the report. Two of them read: “You good Jonny boy?” and “You doing good?” The report says “based on the evidence, it also is our view that it is more probable than not that Tom Brady (the quarterback for the Patriots) was at least generally aware of the inappropriate activities of McNally and Jastremski involving the release of air from Patriots game balls.”

Brady submitted to an interview with investigators, but would not hand over documents, text messages or e-mails. In his interview he said that before the events of the AFC Championship game, he did not know who McNally was or what his job was. The report shows inconsistencies with Brady’s version of events. Jastremski told investigators that Brady did in fact know McNally, and McNally told NFL Security that Brady himself told him what his inflation preference was.

On Jan. 23, the NFL appointed Ted Wells, an attorney who also investigated the Dolphins’ locker room harassment situation in 2013, and league Vice President Jeff Pash to head an investigation into Deflategate. Wells worked with the law firm Paul, Weiss, Rifkind, Wharton & Garrison to draft the report. Investigators interviewed 66 people, including 24 officials, five ball boys, two representatives from Wilson Sporting Goods, as well as Brady, Belichick, Colts general manager Ryan Grigson, Ravens special teams coordinator Jerry Rosburg, and Ravens defensive coordinator Dean Pees.