President Obama's new pick to run the Pentagon will face a dizzying set of challenges affecting the Defense Department's mission, budget and culture.

Defense Secretary Chuck Hagel's resignation Monday comes at a time when the military advance of the Islamic extremists in Iraq and Syria is prompting some fundamental reassessments of defense policy and the use of the military.

"The hardest question before the new secretary — and it's a question the American people are also grappling with — is exactly how much responsibility does the United States have to take for all the problems in a chaotic world?" said Mieke Eoyang, director of the national security program at Third Way, a think tank in Washington.

Related: Defense Secretary Chuck Hagel to step down

"I think the resurgence of ISIS over the fall is what is leading the White House to reevaluate that," she said referring to the Islamic State in Iraq and Syria.

It remains unclear who Obama will pick to serve as his fourth Defense Secretary. Hagel has agreed to remain in office until his successor is confirmed by the Senate, which will likely be early next year. The front runner is Michele Flournoy, former undersecretary of defense for policy. If selected, she would be the first woman to lead the Defense Department.

The new secretary will be drawn into an intense debate inside the military and the White House about operations in Iraq and Syria. There's disagreement about the number of U.S. troops and type of operations needed to defeat the Islamic State. Top officials are also debating the nature of the aid the U.S. should provide to the Iraqis and whether money and weapons should be supplied only through the Iraqi government or directly to the Kurdish forces or the Sunni tribal militias.

Related: McCain: Hagel 'frustrated' with national security policies

"There's a lot of policy to resolve," said one former military official.

Politically, Obama's pick may face a bruising battle in the Senate, which in January will be under Republican control for the first time in eight years. The head of the Armed Services Committee will likely be Sen. John McCain, R-Ariz., a fierce critic of the Obama administration who would use the confirmation process to pressure the White House on foreign policy.

After confirmation, the new secretary will be immediately thrust into another budget crisis. The 2016 budget — due for release early next year — will reignite fears about the budget caps known as sequestration. The two-year deal that temporarily eased the impact of sequestration will expire next year.

Related: Possible SECDEF replacements for Hagel

A new secretary may come to appreciate the newly empowered GOP, which could give the Pentagon more money, potentially lifting one of Hagel's biggest constraints.

"The irony is that the Republicans are taking over Congress and may repeal sequestration. And that would make it easier for his successor to deal with things," said Larry Korb, a defense expert at the Center for American Progress.

A new secretary will also be coming into the Pentagon at a critical moment in the debate about military compensation. The Military Compensation and Retirement Modernization Commission will issue a massive report about troops pay and benefits, along with proposed legislation, in February.

The commission was created by Congress to help jump-start reform on the controversial topic and the new secretary's public position on proposed changes will help shape the debate on Capitol Hill.

The new secretary will also likely oversee a critical transition regarding the integration of women into combat units. The services will complete that transition next year or, if service leaders want to keep some jobs or units off limits to women, service leaders will have to provide the secretary with a detailed request an exemption to the new policy.

About Andrew Tilghman

Andrew Tilghman is the executive editor for Military Times. He is a former Military Times Pentagon reporter and served as a Middle East correspondent for the Stars and Stripes. Before covering the military, he worked as a reporter for the Houston Chronicle in Texas, the Albany Times Union in New York and The Associated Press in Milwaukee.

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