Brady’s Revenge? A win over the Falcons Sunday would be sweet for the Patriots quarterback (Matt Slocum/AP)

When Atlanta Falcons offensive coordinator Kyle Shanahan realized that his playbook for Sunday’s Super Bowl had gone missing amid the din of an NFL gala this past week at Houston’s Minute Maid Park, it was easy for some to assume that the New England Patriots somehow were culpable. The Patriots, after all, are the franchise whose record of suspect behavior includes illegally videotaping opposing coaches’ signals, unexplained technology outages for visiting teams and, of course, the controversy over allegedly doctored footballs that has dogged the team, and the NFL, for two years.

As it turned out, the playbook had been inadvertently picked up by a Bay-area sports writer working his 39th Super Bowl; the writer had mistaken Shanahan’s backpack for his own when leaving a group interview with the Falcons coordinator. With a few frantic phone calls, the mix-up soon was sorted out.

But given the cloud of suspicion that rightly or wrongly always seems to follow the Patriots, they seemed the likely suspects in a mistaken case of shenanigans aimed at getting an unfair edge.

The NFL’s Deflategate scandal was formally resolved on July 15, following 18 months of allegations, rebuttals, investigative reports and legal wrangling. It ended when Patriots quarterback Tom Brady announced he was abandoning his legal challenge to the league’s four-game suspension for his alleged part in an unproven scheme to improperly deflate footballs before the 2015 AFC Championship.

But more than six months later, on the NFL’s biggest, gaudiest, most celebratory and self-congratulatory weekend of the year, Deflategate is the narrative that won’t go away as 140,000 fans stream into Houston and players prepare to take the field Sunday at NRG Stadium for Super Bowl LI.

Deflategate — and the NFL’s handling of it — has stoked Brady’s quest for on-field vindication, if not outright revenge. It has galvanized Patriots fans. It has set up the prospect of a Super Bowl trophy presentation that could stretch beyond awkward if NFL Commissioner Roger Goodell is faced with presenting the Vince Lombardi Trophy to Patriots owner Robert Kraft, whom he assessed a $1 million fine and docked two draft picks in the controversy. And it has been mocked by publications such as The Onion, which recently posted a satirical NFL-sponsored “contest” in which the winner gets to watch Sunday’s Super Bowl from the commissioner’s suite, present the Super trophy to the winning team and shake the MVP’s hand while Goodell watches from home.

Sunday’s game between the Patriots and the Atlanta Falcons ought to put Deflategate drama to rest. Regardless of the outcome, both the Patriots and the NFL already claim victory in the long-running legal battle.

Deflategate’s cost

The saga began when a report surfaced on Jan. 18, 2015, that the Patriots had used deflated footballs in their 45-7 victory over the Indianapolis Colts in the AFC championship game; the report said the footballs were below the minimum standard (12.5 PSI), presumably to give Brady a competitive advantage. Amid vehement denials by Brady, Kraft and Patriots Coach Bill Belichick, the NFL confiscated all 11 football used by the team, found all underinflated and ordered an investigation that concluded it was “more probable than not” that a willful rules infraction occurred.

Kraft accepted the franchise’s costly punishment — believing that paying the $1 million fine and surrendering a first- and fourth-round draft pick would soften Brady’s suspension or possibly get it waived entirely. It didn’t, so the NFL Players Association took Brady’s case to Federal District Court in Manhattan and won. The league appealed, and the federal appeals court ruled in its favor, reinstating the suspension. That left Brady’s legal team with no recourse but the Supreme Court. At that point, the quarterback stood down, accepting the four-game banishment.

Nonetheless, the players association claims Deflategate was a victory on two points.

“Every player in the NFL and every fan now understands the role of our union in protecting the rights of players, no matter what,” said George Atallah, assistant executive director of the NFLPA. Moreover, he argued, former president Barack Obama’s widely publicized quip at a 2015 Labor Day rally in Boston — “If Brady needs a union, we definitely need unions” — underscored for a broader audience the vital role that unions play for workers.

NFL officials declined to comment for this story. But one league official, speaking on a condition of anonymity because of the topic’s sensitivity, said that it was imperative the league appeal the initial verdict because what was at stake was a four-decades’ old, mutually agreed-upon process of meting out player discipline. Whether Goodell was too meek or overly punitive with Brady can be debated, the official said. What was inviolable, he argued, was a disciplinary process that was collectively bargained between the NFL and NFLPA and had been affirmed by both parties as recently as 2011.

What, then, was the ultimate cost of the NFL’s legal victory?

In pure monetary terms, the NFL spent between $2.5 and $3 million to finance an independent investigation and legal costs for the league, the team and players union were estimated to have been significantly higher.

Chicago-based sports business analyst Marc Ganis points to the roughly 10 percent drop in NFL TV ratings at the season’s outset as one. Brady’s absence for the first four games of 2016, Ganis believes, was partly responsible, along with the retirement of quarterback Peyton Manning and suspension of Pittsburgh running back Le’Veon Bell.

In the eyes of many fans, the league’s image — and that of Goodell — as fair and evenhanded took a beating as what began as an attempt to uphold the value of fair-play took on characteristics of a personal attack.

Said Ganis: “You have great fans in New England — among the best in the NFL. Passionate. They love their team; they love Tom Brady. And you had them looking at the commissioner as their opponent and the league office as their opponent.”

‘What’s right for the league’

Atallah, the NFLPA executive, doesn’t believe Deflategate alone chipped away at Goodell’s credibility. He believes it’s merely one in a string of missteps by the NFL front office that has shaken fans’ confidence. “The Brady case and the Deflategate drama was merely the most recent example of the league making mistakes that took most of the NFL fans — and certainly Patriots fans — for fools,” Atallah said.

A petition calling for Goodell’s ouster includes a long list of fans’ grievances against the commissioner. Among them: overreaching his authority, taking “the fun out the game,” waging a vendetta against Patriots, failing to force players to stand for the national anthem and using Deflategate to divert attention from the concussion issue.

Wednesday in Houston, the commissioner’s annual Super Bowl news conference lacked that level of acrimony. But there was no shortage of questions about Goodell’s judgment in handling of Deflategate or his perceived cowardice in staying away from the Patriots’ Gillette Stadium all season.

Goodell explained that while he understood the passion of Patriots’ fans on the issue, he was driven not by passion but by a responsibility to uphold the NFL’s integrity and rules for all 32 teams. As Kraft looked on from the front row, Goodell cast the conflict as simply a disagreement between business partners.

“It’s not all personal [in] nature, which I know people like to make it,” Goodell said. “But for us, it’s about making sure we do what’s right for the league long term.”

“Personal” is surely how it Deflategate seemed to former Patriot Tedy Bruschi, a three-time Super Bowl champion-turned ESPN analyst. “This was a unique distraction mainly because I think it was targeted at one person, and it was targeted at Tom,” Bruschi said in a conference call this week, adding that he believed the experience had deepened the Patriots’ resolve.

Brady, 39, certainly never played better over a four-game stretch than he did upon his Oct. 9 return from suspension, leading the Patriots to victories over Cleveland, Cincinnati, Pittsburgh and Buffalo in succession while throwing 12 touchdown passes and no interceptions along the way, and averaging a 132.2 quarterback rating.

Still, there’s no doubt the first-ballot NFL Hall of Famer has been damaged by the controversy. It can’t be expunged from his biography, nor from the minds of NFL fans who will always regard him as a cheat.

While Brady has spoken with his sterling play, his father laid bare his animus toward Goodell during Super Bowl week in an interview with San Francisco’s KRON 4 News. “He went on a witch hunt and went in way over his head and had to lie his way out numerous ways,” Tom Brady Sr. said, adding that his son was ultimately suspended not for proven wrongdoing but because the court upheld Goodell’s right to do so.

The sad truth is that Deflategate could have been avoided, had the NFL and Patriots reached a settlement following the NFL’s investigation. But both sides dug in, their integrity at stake. And what played out in the public and in court proved costly for both.

Speaking to a handful of reporters during the gala that kicked off Super Bowl LI proceedings, Kraft said he wanted to share a piece of advice from the Old Testament when the topic of Deflategate was raised. He quoted: “There is nothing bad that happens that doesn’t have good associated with it.”

Deflategate had galvanized the Patriots, he said, and brought them to this special moment — a chance to compete for a fifth Super Bowl championship. It’s a moment he intends to savor.

Then, Kraft offered a final thought.

“Jealousy and envy are incurable diseases,” he said. “That’s the way of the world. And we’ll try to take it in and turn it into something that’s an advantage.”