Gen. John Allen Resigns, Forfeiting Potential NATO Nomination

Former top general in Afghanistan resigned Tuesday, White House says.

U.S. Marine Corp. Gen. John Allen speaks to the media in the Pentagon briefing room, on May 23, 2012, in Arlington, Va.

U.S. Marine Corp. Gen. John Allen speaks to the media in the Pentagon briefing room in Arlington, Va., May 23, 2012.

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Marine Gen. John Allen has officially retired from the U.S. military, confirming speculation that the former top general in Afghanistan would not seek NATO's top position.

President Barack Obama met with Allen on Tuesday to formally accept his request to retire so the former ISAF commander can "address health issues within his family," according to a White House media release. Allen turned over leadership of the International Security Assistance Force to Marine Gen. Joseph Dunford on Feb. 10 after more than a year and a half of command.

"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," Obama said in a released statement.

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"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. 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," he continued.

Allen cited unspecified personal reasons for his decision to retire after 38 years with the Marine Corps.

"My primary concern is for the health of my wife, who has sacrificed so much for so long," he said in a written statement. "For more than 35 years, my beloved Kathy has devotedly stood beside me and enabled me to serve my country. It is profoundly sobering to consider how much of that time I have spent away from her and our two precious daughters. It is now my turn to stand beside them, to be there for them when they need me most."

He plans to return to his home in Virginia to take care of his family, he added.

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The Pentagon began investigating Allen last November after the FBI uncovered E-mails classified as "inappropriate communications" between Allen and Jill Kelley, a woman living in Tampa, Fla., who served in an unpaid role at MacDill Air Force Base in Florida, home of U.S. Central Command.

Kelley reportedly received threatening E-mails from Paula Broadwell, who was having an extra-marital affair with then-CIA Director David Petraeus, himself a retired ISAF commander, which eventually lead to Petraeus's resignation.

Allen was on the short list for NATO's top position of Supreme Allied Commander Europe—a position that requires confirmation from the U.S. Senate—when his E-mails with Kelley surfaced.

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The Obama administration put his nomination on hold pending the results of the Pentagon investigation. Allen was cleared of any wrongdoing at the end of January.

Outgoing Defense Secretary Leon Panetta referred to Allen as "one of the United States military's most outstanding battlefield leaders, a brilliant strategist, and an exemplary Marine."

"His leadership over the last 19 months will long be remembered as pivotal to this campaign," said Panetta in a written statement. "The strategy he developed and implemented has put us on the right path towards completing this mission, with Afghan forces now on track to step into the lead for security nationwide this spring and to assume full security responsibility by the end of next year."

"He has earned the lasting thanks of this nation for carrying the heavy burden of leadership with utmost professionalism and courage," Panetta continued. "I wish him and his entire family all the best in the next chapter of their lives."

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Corrected on : Update (02/19/13): This story has been updated to include statements from John Allen and Defense Secretary Leon Panetta.