General John Allen Salutes…His Wife

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Alex Wong / Getty Images

General John Allen testifies last March in Washington with his wife, Kathy, sitting behind him.

Marine General John Allen – caught up and cleared in the email scandal that brought down CIA director David Petraeus – told President Obama on Tuesday he would rather retire from the U.S. military than become Supreme Allied Commander, Europe, one of the top posts in the U.S. military.

“Today, I met with General John Allen and accepted his request to retire from the military so that he can address health issues within his family,” Obama said in a statement. “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 had already tapped Allen for the NATO post last year when former Army general Petraeus’ affair with his biographer, Paula Broadwell, became public and forced him to resign from the CIA. Within days, emails between Allen and Jill Kelley, a Tampa socialite, surfaced. She had gone to the FBI to complain about harassing emails she said she was getting from someone, later identified as Broadwell, concerning Petraeus.

The email exchange — said to involved thousands of pages of messages and attached documents — led Defense Secretary Leon Panetta to put Allen’s nomination on hold until the propriety of the emails was established. Allen was cleared of any wrongdoing last month.

Pentagon officials say Allen had been considering retirement ever since his nomination was placed on hold and his wife, Kathy, has grown increasingly ill with an auto-immune disorder. “For more than 35 years, my beloved Kathy has devotedly stood beside me and enabled me to serve my country,” Allen said in a statement released Tuesday. “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.” Allen, 59, stepped down from the Afghan post Feb. 10.

Panetta praised the longest-serving U.S. commander in the Afghan war – and won who had won Obama’s confidence – last week. “History, when it looks back on the Afghanistan War, will look at the role played by John Allen and see it as pivotal, in terms of the direction that changed while he was in command, and the direction that was set by him has put us on the path towards completing that mission,” Panetta said.

“He’s been under tremendous amount of pressure, a lot of challenges, a lot of, you know, work that he’s had to engage in, a lot of policy decisions he’s had to work on in terms of the recommendations,” Panetta said, without referring to the cloud that had hung over Allen for more than two months.

But fellow Marine general James Amos didn’t hesitate to acknowledge the cost of the scandal, even if Allen ultimately were cleared. Amos, the Marine commandant, said last week that the email probe took “a pretty heavy toll on John, just because he’s a man of such great integrity, and his integrity was being questioned.” Amos’ name has surfaced as a possible replacement for Allen in the NATO slot.

Panetta said he urged Allen not to rush his decision.  “My recommendation to him was take your time, you know, be with your family, think about what you need to do.”

On Tuesday, he did.