One reason people say Kraft feels betrayed, perhaps the main reason, is that Goodell owes him. He was a strong backer of Goodell to become N.F.L. commissioner. He advised Goodell at every turn, and lavishly praised him. As a member of the N.F.L.’s compensation committee, he was instrumental in pushing Goodell’s compensation from $2.5 million in 2007 to $44 million in 2012. He has been a key figure in every television rights deal and labor negotiation. During the Ray Rice domestic abuse debacle, Kraft was one of the few owners to publicly come to Goodell’s defense. He was — and remains — a powerful owner, who has used that power to buttress the N.F.L. commissioner. The two men also developed a close friendship.

But Kraft owed Goodell as well. The most important example was the Patriots’ 2007 Spygate scandal, in which the team was caught videotaping an opposing coach’s hand signals. Although the Patriots paid a $250,000 fine and forfeited a draft choice — and Coach Bill Belichick was fined $500,000 — Goodell ordered that the evidence the Patriots turned over to the league, including a handful of incriminating tapes, be immediately destroyed. Many of the other owners believed that the Patriots had done far worse than steal signals, and that Goodell’s order to destroy the evidence was a cover-up to help his friend Kraft. They were furious.

In truth, the other owners’ resentment of the Patriots went beyond Spygate. In a league built for parity, the Patriots have become the football version of the old Yankees. They are never rebuilding, and always contending. There was resentment over Kraft’s Svengali-like hold on Goodell. And there was jealousy over the Patriots’ success. Although Kraft runs perhaps the most stable franchise in the N.F.L. — who else has had the same coach for 16 years? — many owners were convinced that the team’s success could only be explained by cheating. With the dour, unlikable Belichick as the coach, it was easy enough to believe. After all, he had run a spying operation.

Deflategate was their revenge. Taken at face value, slightly deflated footballs hardly merit the kind of harsh punishment Goodell meted out. In 2012, the San Diego Chargers were caught using “grip enhancing” towels; a fine of $20,000 was levied, and that was only because an equipment manager was said to have ignored a referee’s instruction. (The fine was later overturned.)

And the underinflated balls — if they were underinflated — certainly didn’t affect the game. In the first half, using the supposedly underinflated footballs, Brady and the Patriots took a 17-7 lead. In the second half, with the balls reset at the legal 12.5 p.s.i., the Pats scored 28 consecutive points, making the final score, 45-7.

But that wasn’t the point. The other owners, feeling that the Patriots had been caught cheating a second time, wanted Goodell to crush them. Indeed, although the N.F.L. denies this, it was made clear to the commissioner that there would be repercussions for him if he went too easy on the Patriots. Once the Wells report was issued, with its faulty science and its circumstantial evidence, Goodell did what he had to do. He lowered the boom on his friend, adviser and protector, Kraft.