After tough year, no end in sight to Pentagon's struggles in new year

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It was a fraught year for the Pentagon in 2013, both in the Middle East and back at home in Washington. Here’s a look at the top five defense stories of the year:

Syrian civil war

The Pentagon appeared poised to launch strikes in Syria in August after the United States said it had confirmed that Syrian President Bashar Assad’s forces had used chemical weapons, thus crossing President Obama’s “red line.”

The Navy first deployed destroyers off the coast of Syria. Then Obama said the United States should take action — but he wanted to get approval from Congress first. The move prompted a backlash from many Republicans and Democrats, and a vote looked like it might fail in the House.

The pivotal vote never materialized. After what appeared to be an offhand comment from Secretary of State John Kerry, the United States and Russia agreed to a plan to destroy all of Syria’s chemical weapons stockpiles, thereby removing the rationale for the United States to attack.

But the near three-year civil war rages on in Syria, and the death toll went into six figures in 2013. The conflict — and the hesitancy of the Obama administration to intervene — was a frequent source of tension between the White House, the military and Republican defense hawks.

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War in Afghanistan

The U.S. military prepared for the endgame of the Afghanistan War in 2013, but much still remains up in the air with only a year to go before the full hand-off of security to the Afghans.

The United States had hoped to have a bilateral security agreement in place at this point, but Afghan President Hamid Karzai is once again proving difficult. Karzai has refused to sign the agreement that U.S. officials thought was a done deal.

Karzai now says he will wait until the presidential elections in the spring. American threats to pull out all troops from Afghanistan if the deal was not signed by the end of the year failed to persuade Karzai to sign the agreement.

The U.S. military will head into 2014 planning to draw down to 32,000 troops by the spring. Then, commanders will be obliged to wait to see what transpires between the Obama administration and Karzai in terms of an agreed post-2014 force.

The United States is, for now, planning to keep 8,000 to 10,000 troops in the country after 2014 for training and counterterrorism missions. But Pentagon officials have said the “zero option” remains a possibility if the security agreement cannot be signed.

Sequestration takes effect

What many said was unthinkable happened in 2013 when the automatic budget cuts under sequestration took effect for the Pentagon. The cuts sparked civilian furloughs and slashed training and readiness — but the effects were not so catastrophic as to convince Congress to completely reverse the cuts.

The budget battles have been a defining feature of Defense Secretary Chuck Hagel’s tenure, as the cuts went into effect on March 1, two days after he started on the job.

The Pentagon received some relief in the year-end budget deal, which provides $31 billion above the sequester caps over the next two years. The additional funds will restore readiness, but Pentagon officials have made clear they see the deal only as a band-aid, with most of the sequester cuts still out on the horizon.

The budget deal also prompted a battle that will spill over into 2014. Service and veterans organizations were furious that the budget deal reduced military retiree benefits to save $6 billion. The groups, along with defense hawks on Capitol Hill, have vowed to repeal those cuts next year.

Military sexual assault

The outrage in Congress over sexual assault in the military escalated in 2013 to make it the biggest issue lawmakers debated during the Defense authorization bill mark-ups.

The issue picked up steam in 2013 when a commander overturned a guilty verdict in a sexual assault case, drawing condemnation on Capitol Hill. Then the Air Force’s sexual assault prevention chief was accused of sexual assault (he was later acquitted in civilian court).

Soon after, a Pentagon study found an estimated 26,000 cases of “unwanted sexual contact” in 2012 — an increase of one-third from 2010. Lawmakers proposed dozens of reforms to change the way the military handles sexual assault, and the Pentagon went along with most of them, with Hagel endorsing stripping commanders’ ability to overturn verdicts. But it was a push from Sen. Kirsten Gillibrand (D-N.Y.) to take cases outside the chain of command that sparked a major political fight that pitted Democrats against one another.

Gillibrand’s proposal to take the decision to prosecute cases away from commanders was staunchly opposed by Senate Armed Services Chairman Carl Levin (D-Mich.) and Sen. Claire McCaskill (D-Mo.), as well as the Pentagon brass.

Gillibrand still managed to convince half the Senate to back her proposal, including Democratic Senate leaders and Republicans such as Sens. Ted Cruz (Texas) and Rand Paul (Ky). The fight between Gillibrand and McCaskill was postponed until 2014, however, after a dispute over amendments to the Defense bill scrapped votes on amendments from both Democrats. The debate is sure to pick back up again in 2014.

NSA surveillance

The National Security Agency’s surveillance activities were under the microscope like never before in 2013, after former NSA contractor Edward Snowden leaked classified documents to the media.

The NSA’s bulk phone-data collection and Internet data surveillance drew major criticism from lawmakers, while the revelations of NSA spying on foreign leaders sparked a backlash abroad.

In Congress, lawmakers moved to restrict or completely prevent the NSA from collecting data from all phone calls made in the United States, and the House narrowly defeated an amendment that would have ended the bulk phone-data collection.

Two competing bills from Senate Intelligence Chairwoman Dianne Feinstein (D-Calif.) and Senate Judiciary Chairman Patrick Leahy (D-Vt.) were introduced in the Senate, and they are likely to get consideration in 2014.

While President Obama and NSA officials defended the agency’s practices as important tools to fight terrorism, the White House’s panel created to study the surveillance surprised many observers by recommending broad reforms.

The White House is now weighing how to move forward with the proposed changes, although it has already dismissed one possibility: Creating two different posts for the head of U.S. Cyber Command and the NSA. At the moment, both bodies are run by Gen. Keith Alexander. He is stepping down next year.