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For now, it appears Loyola of Chicago has saved the sanctity of college basketball with its miraculous run to the Final Four. March Madness has compelled the American sports fan. College basketball, for a couple of weeks, is pure and right.

But the NCAA Tournament will end and president Mark Emmert will have to tackle myriad issues, including an FBI investigation that led to indictments of several coaches for paying recruits or taking money from agents to send players to particular agencies when they turned professional.

It has stained the reputation of college basketball and turned Emmert into an embattled leader of a sport that many observers believe needs a major overhaul and cleansing.

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Emmert was in Boston on Sunday to witness Villanova advance to the Final Four with a 71-59 victory over Texas Tech at TD Garden and acknowledged college basketball needs to improve.

“It absolutely does, especially given the FBI investigation,” he said. “That’s shined a very big light, a very bright light on some elements of this that are really disturbing. You know those rumors have always been swirling around out there for years. But this just laid it out in pretty stark relief. You can’t deny it now. I think in the long run that’s going to be very positive because it’s forcing everyone in college sports to confront it.”

Emmert said a commission led by former secretary of state Condoleezza Rice is researching the FBI findings, as well as other issues such as the NCAA’s relationship with the NBA and whether the NCAA acts appropriately in the enforcement of eligibility of its student-athletes.

The NCAA has been accused of being too harsh on athletes for minor violations while allowing chaos to occur with recruiting in its money-generating sports. Schools such as Oklahoma State, Louisville, and Southern California were forced to suspend athletes or coaches who may have been involved in the FBI sting.

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Why did it take an FBI investigation to expose the NCAA problems? Emmert has been accused of being too lax when it comes to the problems in the major-revenue sports of basketball and football. But Emmert said the NCAA lacks the tools to correctly investigate itself, especially compared with the FBI.

“I don’t think it’s an unfair criticism because the reality is a lot of people don’t know . . . the NCAA is a collection of 1,100 schools and those schools engage in self-policing,” he said. “Because we’re an association, we don’t have subpoena power. We don’t have wiretaps. We don’t have sting operations. We can’t compel a witness to talk if he’s not part of a university, and the FBI has all those tools. So when people say, ‘Well, the NCAA should have known about this’ . . . that’s easy to say and hard to do when you don’t have those tools.

“Our tools are like an investigative reporters’ tools. That’s the silver lining here. The FBI has laid out some facts that while they’re difficult to look at, have to be acknowledged and have to be acted on. That’s on us now. That’s our task.”

Emmert is thinking more progressively than perhaps he did in the past. He said that if a basketball recruit has no interest in attending college, he shouldn’t. The NCAA is unhappy with the one-and-done rule, and the NCAA wants to rid itself of the issues created by recruits who are only going to college because they have no better alternative to getting to the NBA.

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“With basketball, I think that the young man who wants to play professionally, [and] that’s all they want, they don’t really want to go to college . . . there needs to be some better choices for them. If they want to go right into the professional ranks, that opportunity really needs to be available for them. And if they want to go to college and they want to develop their basketball prowess while they are getting their degree, great, we’ve got a great deal for them and they can do that and for those tiny few that can go off and play professionally, good for them.

“We’ve got 5,500 young men playing Division 1 basketball. Of those 5,500 in any one year, there will be a dozen, maybe 25 at the most if you count upperclassmen, that will go out and play professional ball. We write the rules for the 5,500, not for the 25. Those 25 or so, they do need career choices and we’re very supportive of that.”

There has been dozens of ideas circulated about how to compensate college athletes so they aren’t tempted to take payments from agents or get involved in the seedy side of amateur athletics. But the idea of giving salaries to athletes is not even close to being considered.

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Amateur athletics, for as much money as it produced for the schools and coaches, will remain amateur, at least for the athletes, regardless of how much they are tempted by those who don’t exactly respect the “purity” of college sports.

“There’s virtually no interest among university leaders for moving to a model that converts student-athletes to employees,” Emmert said. “I just can’t envision that happening, even though a lot of people talk about it. But we do need to make sure we’re constantly providing students everything they need to be successful, as students, as athletes, helping them with their career, doing all of that, but turning them into employees is not in the cards.”


Gary Washburn can be reached at gwashburn@globe.com. Follow him on Twitter @GwashburnGlobe.