Gen. John Allen

General John Allen will retire due to health issues in his family, by requesting his retirement it ends his nomination to become the NATO supreme allied commander. (Getty Images / March 20, 2012)

Marine Corps Gen. John Allen, the former commander of the U.S.-led coalition in Afghanistan whose nomination to lead NATO was delayed last year while investigators probed his e-mails to a Florida socialite, has retired from the military.

The Naval Academy graduate returned to Annapolis a decade ago to serve as commandant of midshipmen. He was the first Marine to hold the second-in-command position.

Allen's surprise retirement, announced by the White House on Tuesday, came less than a month after the Pentagon cleared him of wrongdoing in his e-mail correspondence with Tampa socialite Jill Kelley.

The FBI discovered the correspondence in the course of an investigation that also uncovered the adulterous affair that led former Gen. David Petraeus to step down as director of the CIA.

After Allen was cleared in January, the White House asked the Senate to take up his confirmation to lead NATO as supreme command in Europe.

But on Tuesday, President Barack Obama said he had accepted Allen's request to retire "so that he can address health issues within his family."

Allen, who is married with two daughters, told the Washington Post that he wanted to focus on helping his wife, Kathy, cope with chronic health issues that include an autoimmune disorder.

"Right now, I've just got to get her well," Allen told the Post. "It's time to take care of my family."

Obama called Allen "one of America's finest military leaders," and said he has his "deep, personal appreciation for his extraordinary service over the last 19 months in Afghanistan."

"General Allen presided over the significant growth in the size and capability of Afghan National Security Forces, the further degradation of al Qaeda and their extremist allies, and the ongoing transition to Afghan security responsibility across the country," Obama said in a statement.

"He worked tirelessly to strengthen our coalition through his leadership of the International Security Assistance Force (ISAF), and to improve our relations with the Afghan government."

At the Naval Academy, where Allen spent, cumulatively, nearly a decade of his 40-year career, he is remembered as a standout midshipman, an award-winning teacher and a transformative commandant who worked to usher in a new era of civility and sensitivity at the training ground for future Navy and Marine Corps officers.

An example: When Allen overheard a platoon of first-year midshipmen shout "kill" during training one summer day, he ordered the word expunged from their vocabulary.

The then-commandant explained that plebe summer, when incoming midshipmen arrive on the yard to acclimatize themselves to academy life and begin preparing for careers as officers in the Navy or Marine Corps, was too early to be thinking about the "kill piece" of military training.

Cmdr. William Marks, an academy spokesman, said last year that Allen had a "very successful tour" as commandant of midshipmen in 2002 and 2003.

The esteem is mutual. Allen wrote last year of "our beloved Academy," which he described as a "shining beacon of honor and pride for our nation" where he "amassed countless memories that sustain me and make me proud."

The commandant, second-in-command to the academy superintendent, is analogous to dean of students at a civilian college. Allen, a 1976 graduate, remains the only Marine to have held the position.

His appointment was celebrated by Marines, some of whom felt that the elevation of one of their own to the job was long overdue. But then-superintendent Vice Admiral John R. Ryan said he chose Allen against a field of Navy officers on his merits.

"I didn't go about picking John to pick a first," Ryan told The Baltimore Sun at the time.

Ryan said he was won over by Allen's record — he had earned three master's degrees, commanded infantry companies, served as military secretary to the Marine Corps commandant and led the Basic School, a training facility in Quantico, Va. — and by changes he had introduced as deputy commandant.