As the Cowboys prepare for six weeks without their prized running back, the NFL's commissioner prepares to potentially face the wrath of its most influential owner—Jerry Jones.

A federal judge’s ruling late Monday night was a win for the authority of the office of the NFL commissioner. But, was it a win for commissioner Roger Goodell himself?

Cowboys running back Ezekiel Elliott lost his latest court battle and now appears poised to serve a six-game suspension for violating the NFL’s personal conduct policy starting this week. At 10:15 p.m., Katherine Polk Failla, U.S. District Judge for the Southern District of New York, denied the NFL Players Association’s request for a preliminary injunction to block Elliott’s suspension after hearing oral arguments from both sides in court on Monday.

Failla allowed for 24 hours for Elliott and his team to consider its options for appeal in the Second Circuit Court of Appeals before her ruling is enforced. But as it stands now, Elliott is going to sit out games against the Chiefs, Falcons, Eagles, Chargers, Washington and the Giants; he’d be eligible to return for the Cowboys’ final three games of the regular season, beginning with a Week 15 contest against the Raiders.

Without Elliott, who has rushed for 690 yards in seven games this season, the Cowboys would turn to Darren McFadden, Alfred Morris and Rod Smith in the backfield, and lean on one of the better offensive lines in the league to continue to open up holes. But there’s no doubt that the Cowboys’ hopes of building on the success of 2016, a goal that is already off to a bumpy start, would become even more challenging without Elliott on the field.

Elliott, in his second NFL season, was disciplined by the NFL after a former girlfriend alleged that he physically abused her last summer in Columbus, Ohio. Elliott was not charged with a crime. This court case is not about his guilt or innocence, but rather, whether or not the NFL followed a fundamentally fair process in punishing Elliott. Perhaps the ruling should come as no surprise: The court that upheld the NFL’s four-game suspension of Tom Brady in Deflategate has appellate jurisdiction over the court that is hearing the Elliott litigation.

Sure enough, in her ruling Failla writes that the Brady decision “rejected arguments similar to those here and ordered confirmation of the arbitration award.” As both Brady and now Elliott have learned, the broad authority granted to the NFL commissioner under Article 46 of the collective bargaining agreement—the person in that office has the power to both issue discipline and hear the appeal, or designate the arbitrator who will do so—is difficult to overcome.

While the NFL has scored a big victory in its latest court battle, it’s not so cut and dried for Goodell himself. In disciplining Elliott, he’s strained his relationship with one of his greatest and most influential allies in Cowboys owner Jerry Jones. As recently as last summer, Jones declared the job Goodell has done as “triple A-plus great” and said he would be commissioner “as far as I can see into the future.” But with a pending contract extension through 2024 for Goodell, ESPN reported this weekend that Jones is leading a coalition of owners that have discussed halting those negotiations.

The ESPN report named myriad reasons, including the ongoing anthem issue that many owners believe is threatening business. But Jones’ displeasure over the league’s, and Goodell’s, handling of the discipline for one of his most important players no doubt is prominent in his mind.

Even more certain is that any game Elliott misses would only serve to stoke the wrath of Jones. He considers himself the most influential owner in the league, even if he hasn’t been able to exert that influence when it comes to how the NFL is handling players kneeling for the national anthem. The question now is, how will Jones exert his power as it pertains to the future of Roger Goodell?

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