The deadline for House members to submit their proposed amendments to the Lower Chamber’s version of the Fiscal Year 2014 National Defense Authorization Act (NDAA) passed on Tuesday, leaving an avalanche of offered changes in its wake. While the House NDAA will still need to be merged with its eventual Senate counterpart in conference committee, many of its provisions will likely find themselves in the final bill.

A total of 291 amendments were sent to the House Rules Committee, which will decide on Wednesday how the floor debate will proceed and how many of these amendments will be discussed. ThinkProgress read through them all so you don’t have to, pulling out some of the amendments that would do the most to improve the bill that moves forward:

1. Repeal the 2001 Authorization for the Use of Military Force (AUMF).

Rep. Barbara Lee (D-CA) frequently touts the fact that she was the only member of Congress to vote against the AUMF when first written in 2001. Now, twelve years later, Lee is still fighting to repeal it, but now she has President Obama’s backing — in principle. Obama has expressed an interest in revising the AUMF before it’s eventual repeal, but Lee’s amendment jumps straight to the end. If passed, it would have the AUMF repealed on Jan. 1, 2015 or when the war ends in Afghanistan, whichever comes first.

2. Set up a framework to close Gitmo.

Rep. Adam Smith (D-WA) serves as the Ranking Member on the House Armed Services Committee, a position from which he has long advocated the closure of the military prision at Guantanamo Bay, Cuba. This year, he and several of his colleagues are attempting to insert language into the NDAA doing just that. While it’s a long shot, if it passed Smith’s amendment would add into the NDAA the Guantanamo Bay Detention Facility Closure Act of 2013, which would lift the ban on transferring detainees into the U.S. for imprisonment or trial and cutting off all funding to the prison after 2014.

3. Add more oversight to the administration’s targeted killing program.

House Armed Services Committee Vice-Chair Rep. Mac Thornberry (R-TX) won passage in committee of his provision to have the Secretary of Defense brief his committee and its Senate counterpart every time the administration conducted a kill or capture operation outside of Afghanistan. Rep. Eliot Engel (D-NY), Ranking Member of the House Foreign Affairs Committee, wants to expand that oversight even further. Under Engel’s amendment, Foreign Affairs as well as the House’s Permanent Select Committee on Intelligence would also have to receive the same briefing, increasing the members of Congress in the know.
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As the international community continues to struggle with how to respond to the ongoing violence in Syria, the Pentagon has developed a new doctrine on how to use military force in preventing and ending mass atrocities.

In August 2012, the Department of Defense updated its doctrine on “Peace Operations,” dictating the recommended procedures for participating in multilateral peacekeeping or peace-enforcing efforts. While the doctrine’s update was completed last year, it remained completely hidden from the public, until the Federation of American Scientists obtained it through a Freedom of Information Act request. In revising Joint Publication 3-07.3, the Pentagon opted to create a new appendix on what they refer to as “Mass Atrocity Response Operations” (MARO).

Going beyond the normal scale of fighting seen in civil wars and other conflicts, mass atrocities according to DOD consist of “widespread and often systematic acts of violence against civilians by state or non-state armed groups, including killing, causing serious bodily or mental harm, or deliberately inflicting conditions of life that cause serious bodily or mental harm.”

The document stresses that the military can and should incorporate MARO considerations into its planning and operations whenever appropriate. To facilitate this, the doctrine lists a variety of considerations military planners and strategists should keep in mind when developing operations, including the requirement for a high degree of situational understanding — knowing precisely who the actors are in the conflict, how they interact, and what other forces are at play — and designing a strategic communications plan to both explain the situation and influence the perpetrators.

It also determines five phases that MARO goes through and provides planners with seven approaches that can be mixed and matched in ending atrocities:

1. Area Security — secure a large area with sufficient force deployed in unit sectors.

2. Shape-Clear-Hold-Build — systematically secure limited areas and expand when able.

3. Separation — establish a DMZ or similar buffer zone between perpetrators and victims.

4. Safe Areas — secure concentrations of vulnerable populations such as IDP camps.

5. Partner Enabling — provide advisors, equipment, or specialized support such as deployment or airpower to coalition partners, host nation, or victim groups.

6. Containment — influence perpetrator behavior with strikes, blockades, or no-fly zones.

7. Defeat Perpetrators — attack and defeat perpetrator leadership and/or capabilities.

Joint Publication 3-07.3 makes clear that the decision on whether a situation should be categorized as “an actual or potential” mass atrocity is one that should be left up to national level leadership. It also includes several warnings about the ways in which any military intervention, even when conducted for the best of reasons, can have unpredictable second- and third-order effects.

“MARO may create moral dilemmas for the PO [Peace Operations] force, including whether potential courses of action to halt a mass atrocity that might assist a perpetrator’s long-term aims,” it warns. Even something as basic as protecting civilians could prove to be detrimental, as if “seen to be defending civilians who are linked to only one of the parties, without adjusting to ensure protection for all civilians, both victims and perpetrators will perceive the PO force as anything but impartial.”

The timing of the release means it comes just as the international community prepares to meet once again in Geneva to determine a course of action in ending the civil war in Syria. So far, the conflict has cost the lives of at least 80,000 Syrians, with the vast majority dead at the hands of Syrian President Bashar al-Assad’s security forces.
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At 2:14 AM on Thursday, the House Armed Services Committee (HASC) passed the National Defense Authorization Act of 2014 (NDAA), a massive $638 billion bill designed to fund all military spending and chart military policy for the for the coming fiscal year. An avalanche of amendments greatly changed the original make-up Chairman Rep. Howard “Buck” McKeon (R-CA) presented earlier this week, eventually passing the committee with a vote of 59-2. Here are some of the provisions in the bill that you should know about before it reaches the House floor:

What’s Good

1. Addresses The Military’s Sexual Assault Crisis

In the light of the multitude of scandals and damning reports of sexual assault within the ranks of the military, the HASC added several provisions to the NDAA that reforms the current military justice system. Under the new language, military commanders will be stripped of their ability to dismiss the findings of courts-martial’s juries, something that the military’s leadership has opposed. Commanders will also be unable to reduce sentences imposed on those found guilty of sexual crimes, as one general did in the case that first launched the renewed interest in the issue in February.

In addition, new minimum sentencing guidelines for sexual assault in the military were included, while also adding rape, sexual assault, or other sexual misconduct to the protected communications of service members with a Member of Congress or an Inspector General, essentially bringing protections for those who report military sexual assault in line with those for government whistleblowers.
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The Pentagon’s former top lawyer said on Wednesday that the death of a 16-year old American in a drone strike in Yemen was effectively an accident, the first time any current or former Obama administration official has made such an admission.

On Wednesday afternoon, Attorney General Eric Holder sent a letter to members of Congress for the first time publicly acknowledging that U.S. drones had killed four American citizens. One of those citizens was Abdulrahman al-Awlaki, the 16 year-old son of radical Muslim cleric Anwar al-Awlaki, who on Wednesday the government also for the first time admitted was killed in a U.S. drone strike for his role in al Qaeda in the Arab Peninsula and alleged participation in attempted terror attacks on the United States.

Jeh Johson, who served as the Department of Defense’s general counsel during President Obama’s first term, appeared on MSNBC last night to discuss Holder’s letter, speaking with host Rachel Maddow. In Holder’s letter, Abdulrahman and two other U.S. citizens are described as not “specifically targeted” in the strikes that took their lives — suggesting that perhaps they were killed in a so-called “signature strike” that targets behavior. But Johnson said he thought Holder’s letter could have been more explicit:

JOHNSON: I think you could remove the word specifically from that sentence.

MADDOW: Not targeted at all?

JOHNSON: Not targeted.

MADDOW: They are effectively saying it was an accident.

JOHNSON: We are effectively saying that they were not targeted as part of those specific operations.

MADDOW: But killed anyway.

JOHNSON: But they were, obviously, killed.

Maddow wondered whether Johnson believed that U.S. culpability meant the family of those killed deserved recourse. “That is a very good question,” Johnson said, “I think you should put that to the Department of Justice.”

Nassar al-Awlaki, the father of Anwar and grandfather Abdulrahman, is in the midst of a lawsuit against the U.S. government, alleging that the killing of his son and grandson was unconstitutional. After yesterday’s revelation, a federal judge asked that government lawyers within the next week file a memo on how Holder’s acknowledgement affects the lawsuit.

Prior to Johnson’s statement, the assumption was that Abdulrahman and his friends were killed in what is known as a “signature strike” or “profile strike.” Under the practice, groups of men between 16-55 who meet a certain profile are often considered legitimate targets, often with the U.S. having no concrete knowledge of their identities. There are indications that the practice will be sharply curtailed moving forward, however, as it seems that the same standards applied to the targeted killing of American citizens will be applied to suspected terrorists writ large.

The military’s sexual assault crisis has been in the headlines consistently for the past two weeks, leading two members of Congress to call on President Obama to take executive action and fix it.

Sen. John Tester (D-MT) and Rep. Chellie Pingree (D-ME) introduced the Ruth Moore Act of 2013 earlier this year to help the victims of sexual assault receive benefits once they leave the military. At present, the burden of proof for victims of rape and sexual assault to qualify for disability benefits for conditions related to their trauma, including treatment of post-traumatic stress disorder, is shockingly high, leaving many men and women unable to receive the care they need. A scheduled hearing on the bill was meant to take place on Wednesday, but has instead been delayed until June 3.

Rather than waiting for the Ruth Moore Act to pass, the bill’s sponsors sent Obama a letter on Thursday calling on him to use his authority as president to act now:

We commend your willingness to work with Congress to address the prevalence of sexual assault in the military. However, given the increasing rate of these assaults and the dramatic implications they are having on our service members, veterans, and their families, we strongly urge you to take further action to confront this crisis. In particular, you have the ability to provide justice for thousands of survivors of service-related sexual trauma by calling for more fairness in the Department of Veterans Affairs (VA) disability claims process, and increasing their ability to access the benefits they desperately need. [...]

Our legislation continues to garner support in Congress and has been endorsed by every major veterans’ service organization. Legislation, however, is not necessary to keep faith with these veterans. In 2010, the VA relaxed evidentiary standards to make it easier for combat veterans suffering from PTSD to get the disability benefits they need. It is past time the VA make a similar regulatory change for MST survivors. And you can direct them to do so.

Sexual assault and rape culture in the military has reached a tipping point in the last two weeks, with multiple stories about officials in positions to prevent assaults being charged or investigated for sexual assault themselves. “We’re losing the confidence of the women who serve that we can solve this problem,” Chairman of the Joint Chiefs of Staff Gen. Martin Dempsey said on Thursday. “That’s a crisis.”
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Ahead of possible major actions from the Pentagon and Congress on sexual assault in the military, the U.S. Army is forced to confront yet another instance of a member of the armed forces involved in a shocking sexual assault scandal.

In the latest incident, the Department of Defense revealed on Tuesday a sergeant first class in the U.S. Army stationed at the Ft. Hood, TX military base is under investigation for sexual assault. Along with allegedly sexually assaulting two of his peers, the the sergeant is being investigated for possibly forcing a subordinate into prostitution. Making matters even worse, the soldier under investigation was assigned as the Sexual Harassment/Assault Response and Prevention (SHARP) program coordinator for an eight-hundred person battalion stationed at the base.

The investigation draws a parallel to a case just last week in which the head of the entire Air Force’s sexual assault response program was himself charged with sexual battery in Arlington, VA. No charges have yet been filed against the individual at Ft. Hood, but Pentagon spokesman George Little issued a statement about DOD’s response to yet another alleged instance of rape culture in the military:

I cannot convey strongly enough [Secretary of Defense Chuck Hagel's] frustration, anger, and disappointment over these troubling allegations and the breakdown in discipline and standards they imply.

Secretary Hagel met with Army Secretary McHugh this morning and directed him to fully investigate this matter rapidly, to discover the extent of these allegations, and to ensure that all of those who might be involved are dealt with appropriately.

To address the broader concerns that have arisen out of these allegations and other recent events, Secretary Hagel is directing all the services to re-train, re-credential, and re-screen all sexual assault prevention and response personnel and military recruiters.

Lawmakers quickly lined up to add their voices to the long list of those condemning the latest outrage and sexual assault in the military writ large. “These allegations only add to the mounting evidence of the need to change our military justice system to better hold perpetrators accountable and protect survivors of sexual assault,” Sen. Claire McCaskill (D-MO) said in a statement. Rep. Howard “Buck” McKeon (R-CA) head of the House Armed Services Committee, said in a statement he was “outraged and disgusted” by the latest reports from Ft. Hood, pointing to his own granddaughter in the Army and the “feelings of worry and doubt” many feel when family members join the service.

Much as last week’s case came just days ahead of the Pentagon releasing its annual report on sexual assault in the armed services, Tuesday’s story broke with major implications for the military on the horizon. Wednesday is the deadline for branches of the armed services to provide their plans for how to integrate women into combat units to the Pentagon. Last year, Chairman of the Joint Chiefs of Staff Gen. Martin Dempsey told reporters that the move could help reduce the number of sexual assaults in the military in the long-run as “the more we treat people equally, the more likely they are to treat each other equally.”
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Just one day after the Air Force’s chief of sexual assault prevention was arrested for sexual assault himself, a new Pentagon report shows a sharp increase in the estimated number of assaults in the military annually.

The report from the Department of Defense’s Sexual Assault Prevention and Response Office for Fiscal Year 2012 found a 6 percent rise in reported assaults over the last year, for a total of 3,374. But much more troubling is the estimated number of sexual assault incidents that were never officially reported. In last year’s report, there were an estimated 19,000 instances, but this year the number has jumped to an unprecedented 26,000 instances of assault, leaving thousands unreported.

The disparity in the total number of instances of Military Sexual Trauma (MST) compared to those fully reported — where the victim fills out an official report and action is taken — can be seen as being due to victims’ fears of retaliation, including possible discharge from service or being overlooked for a promotion. The new results line up with those seen in a 2011 Pentagon health survey released in April. According to that report, more female service members were willing to come forward about sexual abuse and assault, with roughly one in five women saying they were victims of unwanted sexual contact from another member of the military, but under reporting remains a serious issue.

“Sexual assault has no place in the United States military,” Pentagon spokesman George Little said in a statement released Monday night in reponse to news that Lt. Col. Jeff Krusinski, the Air Forces’s chief of sexual assault prevention, had been arrested on charges of sexual assault. “The American people, including our service members, should expect a culture of absolutely no tolerance for this deplorable behavior that violates not only the law, but basic principles of respect, honor, and dignity in our society and its military.”

Despite that pledge, assault and abuse in the military has been under increased scrutiny in recent months, following a series of high-profile scandals. In February, Lt. Col. James Wilkerson was reinstated into service after an Air Force general overturned a jury, voiding Wilkerson’s sexual assault conviction. In 2012, Lackland Air Force base saw 12 instructors investigated for sexual misconduct toward 31 trainees, with at least one trainer sentenced to twenty years for rape and sexual assault. Army Gen. Jeffery Sinclair was likewise charged in 2012 with sexually assaulting a female subordinate, then threatening her career if she went public.
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A report aired on 60 Minutes on Sunday shed light on the under-reported threat combat soldiers faced when sent back out into the theater with a concussion, a decision that has had long-lasting repercussions on American veterans.

For years, concussions have been an invisible and therefore neglected injury within the armed services. At the height of the Iraq War, the standard operating procedure was to have soldiers who had sustained head injuries from the explosion of IEDs or other trauma to go back out into the field soon thereafter. In doing so, these soldiers — suffering from symptoms including severe aches, double vision, and nausea — were put at risk of suffering a second concussion before the first had healed, an event that heightens the chance of permanent brain damage.

Maj. Ben Richards, a retired Army veteran, was one of the soldiers sent back out after a concussion who has now been diagnosed with brain injury. “If I could trade traumatic brain injury for a single-leg amputation, I’d probably do that in a second,” he told 60 Minutes, underscoring the difference between visible injuries and those hidden inside the brain. Before his new diagnosis, Richards was told he instead had Post Traumatic Stress Disorder (PTSD). “If you have PTSD and you are not improving through counseling, then it’s your fault,” Richards said of the stigma that still accompanies such a diagnosis. “It was my fault that I wasn’t getting better.”

Watch the full segment here:

Dr. David Hovda, head of UCLA’s Brain Injury Research Center, tried to explain the severity of even mild concussions on soldiers to the Pentagon in 2008. Instead, he was told it was “bad medicine” to keep soldiers out of the field to rest after a concussion, with an assembled team of Army doctors claiming that, because of the stigma that would entail, allowing for rest before being sent back out would make soldiers worse. Gen. Peter Chiarrelli — then the Vice Chief of Staff of the Army, now an advocate for mental health in the military — chose to side with Dr. Hovda in 2009 anyway, issuing an order saying that all forces who suffered concussions would be pulled from combat until their recovery.

Despite Chiarrelli’s decision, the numbers still aren’t good for veterans. 357,000 veterans — or about 20 percent of those who served in Iraq and Afghanistan — have experienced a traumatic brain injury as of January 2009. Despite that, only 46 percent of those who experienced a mild traumatic brain injury were screened for a concussion. At its peak in 2011, the Department of Defense reported 16 new concussions were inflicted per day.

Last year, the NFL donated $30 million to study concussions, in partnership with the U.S. military. Efforts are also under way to raise some $90 million to construct more brain injury centers along the lines of the National Intrepid Center of Excellence, the military’s most advanced brain injury evaluation center. Nine additional centers would enable the military to care for 9,000 brain injuries per year, the amount of new injuries officials expect as the war in Afghanistan winds down.

Tensions within the Republican Party on foreign policy reemerged on Thursday with Sen. John McCain (R-AZ) taking a broad shot at the vision of Sen. Rand Paul (R-KY) and his allies.

At an event at the Center for New American Security (CNAS), McCain took several not so subtle swipes at Paul’s recent attempts to take on the GOP’s foreign policy orthodoxy and singled out the anti-drone filibuster Paul led in March as an example of Republicans yielding to political pressure to back something easy rather than asking tough questions about foreign policy:

McCAIN: Last month, most Republican senators joined a filibuster to protest the President’s policies on the use of armed drones. Rather than debating the very real issues associated with targeted killings, my colleagues chose to focus instead on the theoretical possibility that the President would use a drone to kill Americans on U.S. soil, even if they’re not engaged in hostilities. As misguided as this exercise was, the political pressures on Republicans were significant and many ultimately did — including many who know better.

While he did not name names, among the more senior Republicans who joined in the filibuster were Senate Minority Leader Mitch McConnell (R-KY) and Minority Whip John Cornyn (R-TX). McCain in the immediate aftermath of the drones filibuster referred to Paul and co-filibuster leader Sen. Ted Cruz (R-TX) as “wacko birds,” a phrase he later apologized for using.

McCain admitted that the GOP needs to change its positions on counter-terrorism and other policies, listing several measures he would be putting forward in the coming weeks and months, including an update to the the 2001 Authorization of the Use of Military Force, which his fellow Republicans are likely to embrace. Others, like revisions to U.S. foreign aid strategy towards Egypt and reining in Defense Department spending on costly and underperforming projects will likely earn him more enmity from various blocs within his party.

The Iraq War debacle and much of the Bush administration’s counter-terror policies led Americans to realize that Republicans were selling junk national security policy. Yet at the same time, the neocon stranglehold on the GOP remains alive and well (a sticking point Mitt Romney was faced with during last year’s presidential election).

Since the election, the Party’s soul-searching on foreign policy has broken into the public as struggles for the future of the party on foreign affairs have been frequent. Various sides have been loosely led by Paul, Sen. Marco Rubio (R-FL) and McCain and none seems ready to yield. And at present, it appears that the fight can only be overcome by adhering to a very slim set of neocon-esque foreign policy principles, or, as Secretary of Defense Chuck Hagel discovered during his nomination battle, face accusations of apostasy and risk internal isolation.

So far, McCain is fine with having the debate, but appears to be wondering whether there is room for his views in the GOP. “Right now the far left and far right in America are coming together in favor of pulling us back from the world,” McCain warned at CNAS. “The President and I have had our differences, many of those differences will persist. But there are times these days when I feel I have more in common on foreign policy with President Obama than I do with some in my own party.”

The Central Intelligence Agency may be out of the armed drones business soon, according to a report out Wednesday morning, possibly granting more visibility to the Obama administration’s targeted killing program.

According to The Daily Beast, the White House is ready to approve a plan transferring authority to launch lethal missions in areas such as Pakistan from the CIA to the Department of Defense. Both DOD and the CIA currently have access to unmanned aerial vehicles, as drones are formally known, but use them in different ways for different purposes under different congressional authorities and different rules of transparency.

Should President Obama sign-off on the idea, the shift that would take place would not likely be immediately apparent to the public, but would go a long way to formalize the procedures in which drones are used. The process known as “institutionalization” has been in motion for over a year now, according to The Daily Beast, headed by newly-confirmed CIA Director John Brennan:

Brennan, who has presided over the administration’s drone program from almost day one of Obama’s presidency, has grown uncomfortable with the ad hoc and sometimes shifting rules that have governed it. Moreover, Brennan has publicly stated that he would like to see the CIA move away from the kinds of paramilitary operations it began after the September 11 attacks, and return to its more traditional role of gathering and analyzing intelligence.

Under the new structure, the CIA would still have a role in providing the intelligence necessary to identify targets, at least temporarily, but would no longer have operational control of lethal missions. That role in gathering intelligence means that the CIA’s use of unarmed drones for surveillance purposes is unlikely to be affected. While not a guarantee of greater transparency, placing the targeted killing program entirely under the Defense Department would mean that it would no longer be “covert” — or both secret and deniable by the government — but instead “clandestine” — meaning the administration would be unable to legally lie about operations.

The move mirrors an approach former Defense Department lawyer Jeh Johnson promoted in an appearance at Fordham University on Monday. Johnson is the latest in a long line of high-profile Democrats questioning the current structure of the targeted killing program and the secrecy surrounding it. In recent weeks, CAP Chair John Podesta, Sen. Ron Wyden (D-OR), and Rep. Keith Ellison (D-MN) have all called for greater openness from the Obama administration about the way the program is carried out.