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.
"He had a couple of ideas on what we could do better in plebe summer," Ryan said. "What impressed me was it wasn't Marine-oriented, it was leadership-oriented."
Allen led a reconsideration of training at the academy, and ordered the end of some of the harsher methods employed by upperclassmen to discipline their younger charges.
Gone was the "spot correction" — the use of push-ups and sit-ups as instant punishment for minor rules violations, the source of the phrase "Drop and give me 20." Some upperclassmen were relieved of their plebe-training jobs after a plebe complained about being screamed at and scolded too harshly.
Allen told The Sun at the time that preparing future officers for combat should not cross the line into humiliation. He said he wanted upperclassmen to lead by example, not fear.
"We never want to denigrate someone, robbing them of their dignity," he said. "We want parents to understand that when they give us their children, they will be treated very fairly."
Academy officials said the changes were aimed at making training smarter, not gentler. And the brigade appeared to respond; an anonymous survey of nearly 3,000 midshipmen near the end of Allen's first year showed a greater feeling of security and belonging among women and minorities and a declining sense that athletes who broke rules were receiving more lenient discipline than other students.
Allen's tour as commandant was his third at the academy. Raised on his father's stories of Navy service during World War II, the Virginia native arrived at Annapolis in 1972, and would rise to command half of the brigade of 4,000 students. He graduated in 1976 and was commissioned a second lieutenant in the Marine Corps.
After commanding rifle and weapons companies, studying at the Defense Intelligence College and completing a fellowship at the Center for Strategic and International Studies, he returned to Annapolis in 1988 to teach political science and train paratroopers as jump master of the academy.
In 1990, he earned the William P. Clements Award as military instructor of the year, and left to direct the Infantry Officer Course at the Basic School.
He would go on to serve in the Caribbean and the Balkans and, after his tour as commandant of midshipmen — and promotion to brigadier general — in Iraq and Afghanistan.
Allen succeeded Petraeus as commander of the Tampa-based U.S. Central Command in 2010 and as commander of the International Security Assistance Forces in Afghanistan in 2011.
In Iraq, Allen won praise for ability to work with tribal leaders in the volatile al-Anbar province. He is credited with holding the mission in Afghanistan together amid several challenges. The burning of Qurans by U.S. troops and images of Marines urinating on the corpses of Taliban fighters enraged Afghans, and attacks on international forces by the Afghan fighters they're supposed to be training have increased.
Admired by Republicans and Democrats, he was seen as a lock to win confirmation to head U.S. European Command until the FBI discovered the alleged emails to Kelley.
Agents discovered the messages while investigating harassing emails to Kelley, allegedly from 40-year-old Paula Broadwell, Petraeus' biographer and reported mistress.
Petraeus, the architect of the surges in Iraq and Afghanistan, acknowledged an affair and resigned as director of the CIA.
The messages from Allen to Kelley, which officials described as "flirtatious" and "inappropriate," led the Obama administration to delay his Senate confirmation hearing as head of U.S. European Command and supreme allied commander Europe.
Colleagues said the communications had been misconstrued, and Secretary of Defense Leon Panetta cautioned against jumping to conclusions.
Panetta ordered the Defense Department's inspector general to investigate the correspondence. But he also told reporters that Allen "certainly has my continued confidence to lead our forces and to continue the fight."
The inspector general cleared Allen last month of any wrongdoing, and the White House asked the Senate to schedule a confirmation hearing.
His retirement Tuesday now leaves the administration to look for a new candidate for the job.