The top military leader spoke exclusively with The Post’s Rajiv Chandrasekaran about why he's deciding to step away from service. (The Fold/The Washington Post)

Four months after taking office, President Obama approved the firing of the four-star Army general leading the war in Afghanistan. The following summer, the president sacked his replacement, Army Gen. Stanley A. McChrystal, for making intemperate remarks to a reporter. McChrystal’s successor, Army Gen. David H. Petraeus, often disagreed with Obama on troop levels and war strategy.

It was not until Marine Gen. John R. Allen took command of the war in July 2011 that Obama found a general with whom he clicked. Allen demonstrated more flexibility on troop numbers and shifts in strategy than his predecessors. Obama’s aides, in turn, were far more willing to listen to Allen’s views on how the war needed to be waged.

Obama had wanted to give Allen, who relinquished command in Kabul this month, the military’s most prestigious overseas assignment — supreme allied commander in Europe. But on Tuesday morning, Allen announced that he planned to retire from the military because his wife is seriously ill.

The decision deprives the president of a four-star general with whom he had built a close wartime relationship and forces the White House to find a new candidate to oversee U.S. and NATO operations in Europe.

“I told General Allen that he has my deep, personal appreciation for his extraordinary service over the last 19 months in Afghanistan, as well as his decades of service in the United States Marine Corps,” the president said in a statement after meeting with the general at the White House.

Gen. John R. Allen says goodbye to U.S. and Afghan troops during his last visit to southern Afghanistan. (Photo by Master Sgt. Kap Kim/PHOTO BY MASTER SGT. KAP KIM/COMISAF PUBLIC AFFAIRS)

In an interview Monday evening, Allen said he wants to focus on helping his wife, Kathy, cope with a combination of chronic health issues, which include an autoimmune disorder.

“Right now, I’ve just got to get her well,” Allen said. “It’s time to take care of my family.”

In Afghanistan, Allen oversaw the strategic shift from troop-
intensive counterinsurgency operations to the development of local security forces. As he orchestrated that change, he managed the removal of 33,000 U.S. troops from the country and the response to a spate of attacks on coalition personnel by members of the Afghan security forces.

Allen, who relinquished command of the war nine days ago, said his decision was not influenced by a Pentagon investigation into e-mail messages he exchanged with Tampa socialite Jill Kelley, who was involved in the scandal that prompted Petraeus to resign as CIA director last year. Allen was cleared of wrongdoing last month after investigators combed through the messages.

Although senior Defense Department officials described the content of some of the missives as racy and flirtatious, the Pentagon’s inspector general determined that Allen had not violated military prohibitions against conduct unbecoming an officer. Allen’s allies have described the investigation as overblown, arguing that his e-mails to Kelley, which included words such as “sweetheart,” reflected nothing more than friendship.

The messages were uncovered during an FBI investigation into a set of harassing e-mails Kelley had received. The bureau eventually determined that those messages had been sent by Petraeus’s biographer, Paula Broadwell, and that Petraeus and Broadwell were having an affair.

“The investigation took a toll on her,” Allen said of his wife.

He said that his wife’s condition has been deteriorating for a few years and that he thinks it would have been problematic for her to receive the necessary medical authorization from the military to travel to Belgium, where NATO is based. The couple’s two adult daughters, who have helped to care for Kathy Allen, also live in Northern Virginia.

“For a long time, I told her, ‘When you can’t bear this anymore, just tell me and I’ll drop my [resignation] letter right away,’ ” Allen said. But he said he no longer wants to place the pressure of that decision on her. “Now I need to be the one who takes this out of her hands.”

Allen, 59, was the first Marine ever selected to command a theater of war. Leading the multinational military campaign in Afghanistan was “the honor of a lifetime,” he said.

He said the strategic shift away from counterinsurgency, the withdrawal of U.S. troops, the attacks by Afghan security forces and the months-long closure of supply routes through neighboring Pakistan “tried to wrench the campaign off the tracks.”

“We managed to hold on, but it was a herculean effort,” he said.

Even so, violence in Afghanistan is higher than it was before Obama ordered a surge of U.S. forces into the country, according to the most recent Pentagon assessment. The report also stated that just one of the Afghan army’s 23 brigades is able to operate without support from the U.S. military or NATO allies, making it difficult for the Afghans to take the lead in fighting the Taliban despite U.S. efforts to hand over that responsibility.

The path to the president’s decision to withdraw 34,000 U.S. troops from Afghanistan by February 2014, announced during last week’s State of the Union address, illustrates the relationship between Obama and Allen, according to senior U.S. officials familiar with the matter. Allen’s staff had recommended that no more than 25,000 troops be removed this year, an assessment the general initially supported.

But when the White House made it clear to Allen that the president wanted to remove half of the 68,000 troops now in the country, the general developed a plan to satisfy Obama: Allen recommended the withdrawal of 34,000 troops, but he also asked Obama to push the deadline back by two months — from the end of the year to February 2014, allowing his successor, Marine Gen. Joseph F. Dunford Jr., to avoid pulling out more than 25,000 troops by the autumn, when Taliban fighters typically begin their winter rest.

Obama concurred with Allen’s plan. That allowed both parties to get what they wanted: White House officials could say that the decision to remove 34,000 troops was in line with Allen’s recommendation, while the general could remain close to his initial withdrawal target.

Allen, a native of Warrenton, was the first Marine to serve as the commandant of midshipmen at the Naval Academy. He spent two years in Iraq’s Anbar province, where he led an effort to reach out to Sunni tribal leaders to try to persuade them to stand against al-Qaeda militants — a shift that helped turn the course of the war in western Iraq.

Allen informed Defense Secretary Leon E. Panetta several weeks ago that his wife’s condition might lead him to decline the Europe nomination, but Allen said he did not come to a final decision until the past few days.

His command responsibilities and other military assignments have kept him away from home for much of the past decade. He had only a week of leave between his Iraq and Central Command jobs and only a week off before he went to Afghanistan, much of which was spent moving and preparing for his confirmation hearing. He said he and his wife have not had a vacation since their daughters were young.

“All I am seeking now is time with Kathy,” he said. “I want to be home on a regular basis.”

To view a gallery of photos and an interview with Chandrasekaran on The Fold, go to