John R. Allen Resigns as Brookings President After Qatar Revelations

John R. Allen, the retired four-star general who once commanded American troops in Afghanistan, resigned on Sunday as president of the Brookings Institution, six days after a court filing revealed evidence that he had secretly lobbied for Qatar.

His resignation is the latest indication of the seriousness of the federal investigation involving the general. Brookings, a 106-year-old research center and a pillar of Washington’s liberal establishment, had placed General Allen on administrative leave last Wednesday.

“The integrity and objectivity of Brookings’s scholarship constitute the institution’s principal assets, and Brookings seeks to maintain high ethical standards in all its operations,” Glenn Hutchins and Suzanne Nora Johnson, the co-chairs of the institution’s board of trustees, wrote on Sunday in an email to the staff. “Our policies on research independence and integrity reflect these values.”

In a statement, General Allen said: “While I leave the institution with a heavy heart, I know it is best for all concerned in this moment.” His statement made no reference to the filings or any investigation.

The newly disclosed filing that prompted the resignation was an application in April by federal prosecutors for a warrant to search General Allen’s electronic communications. In the application, prosecutors cited messages General Allen had sent apparently seeking payments for work to help Qatar win Washington’s backing in a feud with its regional rivals, Saudi Arabia and the United Arab Emirates.

In the spring of 2017 those rivals led a push to strangle Qatar by cutting off diplomatic ties and blocking trade with the country, accusing its government of supporting extremism.

Qatar hosts a major American air base, and General Allen, who had recently left government, appears to have sought a $20,000 payment billed as a “speaker’s fee” for a weekend trip to advise Qatar’s rulers on the crisis.

The filing quoted messages from General Allen seeking to “work out a fuller arrangement of a longer-term relationship” and attempting while on the same trip to advance business deals with Qatar for two companies with which he was affiliated.

Prosecutors also charged in the filing that General Allen lied about his role and withheld evidence sought by a subpoena.

A spokesman for General Allen last week called the narrative presented in the filing “factually inaccurate, incomplete and misleading.”

The spokesman, Beau Phillips, said in a statement that the general had done nothing wrong or unlawful, had never acted as an agent of Qatar or any foreign government, and had never obstructed justice.

General Allen was enlisted to travel to Qatar by Richard G. Olson, a former U.S. ambassador to the United Arab Emirates and Pakistan, and Imaad Zuberi, a business executive with ties to the Middle East. Mr. Olson has agreed to plead guilty to violating a prohibition against lobbying for a foreign government in the period immediately after leaving diplomatic service.

Mr. Zuberi, who paid for the Qatar trip, is serving a prison sentence for violating foreign lobbying, campaign finance and tax laws, as well as for obstruction of justice.