SYRACUSE, N.Y. — Jim Boeheim became the face of Syracuse University over the past five decades, first as player, then as coach – revered for wins and delivering a national title to a struggling city in 2003. But the coda to his decorated career has become tinged with undeniable blemishes, laid out in harsh penalties for violations the NCAA says show Boeheim and the university lost control of athletics.

Boeheim and Syracuse officials acknowledged the unwanted ties Wednesday in announcing he will retire after three more seasons, while insisting they don’t agree with parts of the scathing NCAA report and will appeal to try to save scholarships and wins.

Syracuse coach Jim Boeheim will retire in three years following punishment from the NCAA for violations that lasted more than a decade. The Associated Press

Syracuse University Chancellor Kent Syverud said Boeheim decided to make the announcement to “bring certainty to the team and program in the coming years” and to allow for a smooth transition.

“Coach Jim Boeheim has been a mainstay at Syracuse University for more than one-third of our entire 144-year history,” Syverud said in a statement. “He enrolled as a student here in 1962 and has never left. He has been the embodiment of Orange pride.”

When Boeheim turned 70 in November, wife Juli asked him if he was OK with coaching as a septuagenarian and all that goes along with it.

“I just think one day you’re going to have to slow down,” Juli said. “He doesn’t want to, number one, and he feels better than he ever has.”

There’s been a change of heart.

The violations, lasting more than a decade under Boeheim’s watch, involved academic misconduct, extra benefits and the university’s drug-testing policy, according to a March 6 report by the NCAA Committee on Infractions. Boeheim is already suspended for the first half of the next Atlantic Coast Conference season, a total of nine games. Syracuse will also have three scholarships taken away for four seasons and all wins vacated in which an ineligible player participated during five seasons from 2004 to 2012. The total wins removed from records could be as high as 108, depending on what happens in the appeal process. Syracuse has already vacated 24 wins.

Athletic director Daryl Gross is also stepping aside, immediately taking a marketing position with the school. Pete Sala will serve as interim athletic director.

Boeheim, who scheduled a news conference for Thursday, has had problems before. The NCAA banned the Orange from the 1993 NCAA Tournament for recruiting violations.

Longtime assistant coach Mike Hopkins, a former star for the Orange, is in line to succeed Boeheim.

In its report, the NCAA placed Syracuse on probation for five years for breaking with the “most fundamental core values of the NCAA.” Athletic department officials interfered with academics, making sure star players stayed eligible, the report said.

The report said the former director of basketball operations, who was picked by Boeheim and whose job primarily consisted of monitoring academic performance of basketball student-athletes, became overly involved. He collected and maintained student-athletes’ usernames and passwords and provided them to others, including student-athlete support services.

Members of the support staff routinely accessed and sent emails from student-athletes’ accounts and corresponded directly with professors and included attached course work to maintain the required grades for the student-athletes to remain eligible, the report said.

The 94-page report also said basketball staff encouraged students to develop relationships with a booster, which led to rule violations. The booster provided more than $8,000 to three football and two men’s basketball students for volunteering at a local YMCA, the report said. Additionally, the booster gave money to basketball staff for appearances or assistance at YMCA events, payments that weren’t reported to the school as outside income or supplemental pay, as NCAA rules require.

“The behavior in this case, which placed the desire to achieve success on the basketball court over academic integrity, demonstrated clearly misplaced institutional priorities,” the NCAA said.

Punishment also includes financial penalties and recruiting restrictions for two years.

Syverud reiterated Wednesday that the school does not agree with all of the NCAA’s conclusions.

“The decision to appeal is not taken lightly. We remain disturbed by the severity of certain penalties and the characterization by the NCAA of certain facts surrounding the case,” Syverud said.

Gross, athletic director for a decade, will serve as vice president and special assistant to the chancellor and adjunct professor in the university’s college of sport and human dynamics.

“I am thankful to have worked with what I consider the greatest coaching staff in the country and our student-athletes who have competed proudly at the highest national levels,” said Gross, who led the push for Syracuse to join the Atlantic Coast Conference in 2013 and spurred marketing the Syracuse brand to the metropolitan New York City area, scheduling games at MetLife Stadium in New Jersey against Southern California, Penn State and Notre Dame.

In anticipation of the report, Syverud announced a postseason ban for this year for the men’s basketball team. The NCAA accepted the ban and indicated the school could delay the loss of scholarships for one year. Boeheim has a stellar class coming next fall, rated the best in his long tenure.

The announcement of the changes comes less than two weeks after the season finale. At a postseason banquet the day after the Orange lost at North Carolina State to finish with a record of 18-13, Boeheim, the second-winningest coach in Division I history with 966 victories, told an audience of around 700 fans that he wasn’t about to leave as basketball coach.

“I’m not going anywhere,” he said.

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