MIAMI (CBSMiami) – Seven-hundred and eighty-nine days after Yahoo! Sports published a lengthy investigative piece detailing dozens of allegations against the University of Miami’s athletic department; the school has finally learned its fate from the NCAA.

“The University of Miami lacked institutional control when it did not monitor the activities of a major booster, the men’s basketball and football coaching staffs, student-athletes and prospects for a decade,” the NCAA said Tuesday.

The NCAA said Miami football will not receive an additional bowl ban, but will lose nine scholarships over three years. The basketball program will also lose one scholarship over the next three years and the entire athletic department will be on probation for the next three years.

The school had previously self-imposed a two-year postseason ban as a result of the Shapiro scandal.

“Each case is unique and no doubt folks will have a difference of opinion on whether the penalties were too stiff or too light. In this particular case we felt the institution’s self-imposed penalties were unprecedented and those were factors that weighed into the committee’s thinking,” said NCAA Committee on Infractions chair Britton Bankowsky. “What the self-imposed penalties represented was that the university was taking the case very seriously. It understood it needed to respond internally to the situation. The committee appreciated those decisions and it reflected that in the decision.”

In addition, former University of Miami head basketball coach Frank Haith has received a five-game suspension for his part in the scandal, according to CBS4 news partner the Miami Herald.

CBSMiami.com reached out to the University of Missouri for a comment and is awaiting a response on Haith’s suspension.

Former UM football coaches Clint Hurtt and Aubrey Hill were hit with two-year show cause penalties, meaning they are essentially unemployable for the next two seasons, according to the Herald. Former UM assistant basketball coach Jorge Fernandez also was hit by a show-cause penalty for two years.

Any school that wanted to employ Hurtt, Hill, or Fernandez would have to show cause to the NCAA’s Committee on Infractions why they should be allowed to be hired.

Hurtt is currently on the staff of Louisville’s football team, but no word has come down on what the Cardinals plan to do about the situation.

The NCAA said that several football coaches, three basketball coaches and two athletics department staff members “had a poor understanding of NCAA rules or felt comfortable breaking them. Futhermore, some of the coaches provided false information during the enforcement staff and university’s investigation.”

It’s one of the final acts in a lengthy battle between the school and the NCAA, the NCAA’s Committee on Infractions, and convicted Ponzi schemer and primary UM accuser, Nevin Shapiro.

The story started in 2011, just before the Hurricanes football season was to get underway. That’s when Yahoo! Sports released its work with Shapiro that according to Shapiro would get the school the death penalty when all was said and done.

In August 2011, Shapiro did an exclusive interview with CBS4’s Jim Berry and said then, that the NCAA had in its possession is “going to be so detailed and to the truth that it will be impossible for any former players or current players to go around it.”

Throughout the allegations, investigation, and hearings before the Committee on Infractions, Shapiro sought to portray himself as more of a hero than as a criminal and former booster who inflicted major damage to the school he repeatedly said he completely loved.

“Nevin would rather be known as the guy who established standards and procedures to prevent future people like him from being able to penetrate a school,” Shapiro’s attorney Maria Elena Perez told CBS4 in August 2011.

Shapiro, who is in federal prison, alleged that he paid players, lavished gifts on players, helped coaches pay players, made loans to coaches, and multiple other claims. Shapiro said he had access to players and CBS4 video showed him on the field in front of the team in the tunnel waiting to run out with the team.

Shapiro accused multiple players, including several current NFL stars, of being involved with his benefits scheme. He also said the university was directly at fault because “of the desire to put money first, I was given carte blanche to do things I shouldn’t have been able to do.”

The school quickly tried to distance itself from Shapiro, but multiple players on the 2011 roster were implicated and the school suspended some players and dismissed others. It started a rough two and a half years for the school that has extended more than 100 weeks.

Things started heating up in the case in 2013 when the NCAA had to admit that it committed numerous violations of its own rules while investigating UM. The NCAA publicly admitted the mistakes, had an outside firm investigate the investigation, and continued moving forward with the case.

Earlier this year, the school was given a notice of allegations that detailed the NCAA’s specific charges against the school.

Among the charges was the much-ballyhooed lack of institutional control charge which is the gateway charge to some of the NCAA’s most severe sanctions, up to and including the death penalty which shuts down a program for a defined amount of time.

The school appeared before the NCAA’s Committee on Infractions in June 2013 and emerged from the hearings hoping to hear something within the six to eight week time frame that it usually takes a COI ruling to be handed down.

Instead, the school was left waiting for nearly four months while the NCAA composed its report against the University of Miami that was released Tuesday.

The timing of the release by the NCAA was criticized by UM fans as the Canes had just become bowl eligible the week the sanctions were revealed and less than two weeks before the team’s biggest game of the year against the Florida State Seminoles.

Still, after two-and-a-half years of allegations, waiting, more allegations, and more waiting, the school can finally start to put the entire Nevin Shapiro scandal in the rear view mirror and concentrate on bringing the program back to the top of the college football world.

The school said Tuesday it would accept the penalties from the NCAA and will not seek to challenge them in court, meaning the Nevin Shapiro scandal is finally over.