WASHINGTON — Marine Gen. John R. Allen, the longest-serving leader of U.S. and NATO troops in Afghanistan, asked President Barack Obama on Tuesday to accept his retirement from the military because his wife is seriously ill, a move that nullifies his nomination to be supreme allied commander in Europe.
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," said Allen, who relinquished command of the war nine days ago. "It's time to take care of my family."
Allen, 59, said his decision was not influenced by a Pentagon investigation into email messages he exchanged with Tampa socialite Jill Kelley, 37, who last year unwittingly set off a scandal that led to the resignation of another top general, David Petraeus, as director of the CIA.
Although senior Defense Department officials had described some of the email between Allen and Kelley as racy and flirtatious, the Pentagon's inspector general determined the general had not violated military prohibitions against conduct unbecoming an officer.
Allen's allies have described the investigation as overblown, arguing that Kelley, who is married to Dr. Scott Kelley, 46, sought to ingratiate herself with several generals who served at the U.S. Central Command headquarters at MacDill Air Force Base in Tampa. Both Petraeus and Allen had been leaders at CentCom.
The messages were uncovered during an FBI investigation into 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.
Neither Kelley nor her representatives would comment on Allen's retirement, said Kelley spokesman Gene Grabowski.
In an interview earlier this year with the New Republic, Kelley was asked which she considered the most embarrassing emails in the exchange with Allen.
"Don't get me wrong, some of them are flirtatious," she responded. "I mean we never had an affair, but I guess at two in the morning, when he's e-mailing me, sometimes he'd be flirtatious."
The Tampa Bay Times has filed a Freedom of Information request with the Pentagon's inspector general asking for Allen's emails with Kelley. So far, the IG has not responded.
In other emails obtained by the Times, Kelley tells of an episode last March in which Allen called her from the war to enlist her help in preventing a radio personality from frying a Koran.
In emails to Tampa Mayor Bob Buckhorn, Kelley said Allen was worried the radio stunt could put troops in harm's way.
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"Gen. Allen will be calling me from Afghanistan at 1pm on this — and our next step," she wrote in one message to the mayor.
The stunt never materialized.
In a statement Tuesday, Obama said he had granted Allen's request to retire.
"I told Gen. 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," he 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 NATO post.
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 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.
"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.
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 CentCom 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."
Times staff writers William R. Levesque and Will Hobson contributed to this report.