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Washington - Marine Gen. John R. Allen, the longest-serving leader of U.S. and NATO troops in Afghanistan, asked President Barack Obama on Tuesday morning to accept his retirement from the military because his wife is seriously ill, a move that nullifies his nomination to be the supreme allied commander in Europe.
In a statement, Obama said he had granted Allen's request. "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.
The decision deprives Obama of a four-star general with whom he had built a close wartime relationship and forces the White House to find a new candidate for the military's most prestigious overseas assignment.
In an interview Monday evening, Allen said he wants to focus on helping his wife, Kathy, cope with a combination of chronic health issues that 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 shift, 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 email messages he exchanged with Tampa, Fla., socialite Jill Kelley, who was involved in the scandal that prompted David 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 had described the content of some of 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 Kelley had sought to ingratiate herself with several generals who have served at the U.S. Central Command headquarters in Tampa and that Allen's responses to her, which involved words such as "sweetheart," reflected nothing more than friendship.
The messages were uncovered during an FBI investigation into a set of harassing emails Kelley had received. The bureau eventually determined that those messages had been sent by Petraeus' biographer, Paula Broadwell, and that Petraeus and Broadwell were having an affair.
"The investigation took a toll on her," Allen said of his wife.
Allen said his wife's condition has been steadily deteriorating for a few years and has now reached a point where he believes 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 Virginia.
Even if she could have traveled there, Allen said, his responsibilities would keep him away from her much of the time. The current allied commander, Adm. James Stavridis, travels away from his Belgian headquarters more than half of each month.
"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 for that decision on her. "Now I need to be the one who takes this out of her hands."
Allen, 59, is the first Marine ever to be selected to command a theater war. Leading the multinational military campaign was "the honor of a lifetime," he said.
He said the strategic shift away from counterinsurgency, the withdrawal of U.S. forces, the attacks by Afghan security forces as well as 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 remains higher than it was before Obama ordered a surge of U.S. forces into the country, according to the most recent Pentagon assessment of the war. 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.
A native of Warrenton, Va., Allen also 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.
He eventually became Petraeus's deputy at the Central Command, where his portfolio focused largely on Iran. The job afforded him the opportunity to brief Obama, who grew impressed by the general's analyses. When Obama appointed Petraeus to head the CIA, Allen was tapped to go to Kabul in 2011.
As the top commander in Kabul, Allen forged a far closer bond with Obama than his two most-immediate predecessors, now-retired Gens. Petraeus and Stanley McChrystal. When Obama and Allen walked out of a lunch in the White House last year, the president put his arm around the general, according to administration and military officials. "John Allen is my man," Obama said to staffers waiting in an anteroom.
In his statement Tuesday, Obama praised Allen as "one of America's finest military leaders, a true patriot, and a man I have come to respect greatly."
"I wish him and his family the very best as they begin this new chapter," he said, "and we will carry forward the extraordinary work that General Allen led in Afghanistan."
Allen informed Defense Secretary Leon Panetta several weeks ago that his wife's condition might lead him to decline the nomination to go to Europe, but Allen said he did not come to a final decision until the past few days. He said he needed time to evaluate his wife's condition, and he had hoped it would improve upon his return home.
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 again 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 had not had a vacation since their daughters were young girls.
"All I am seeking now is time with Kathy," he said. "I want to be home on a regular basis."