CIA Director David Petraeus has given his resignation to President Obama today, citing having an extra-marital affair.

Petraeus vacated his rank of General in the U.S. Army to take command at the CIA in 2011 following Leon Panetta’s move to the Department of Defense. Petraeus, the architect of the U.S. counterinsurgency strategy in Iraq, had previously been seen as unassailable politically by many on the right and left.

President Obama issued a statement on Petraeus’ resignation, saying, “By any measure, [Petraeus] was one of the outstanding General officers of his generation, helping our military adapt to new challenges, and leading our men and women in uniform through a remarkable period of service in Iraq and Afghanistan, where he helped our nation put those wars on a path to a responsible end.”

“I am completely confident that the CIA will continue to thrive and carry out its essential mission, and I have the utmost confidence in Acting Director Michael Morell and the men and women of the CIA who work every day to keep our nation safe,” the President’s statement continued.

Petraeus’ wife, Holly Petraeus, also serves in the administration at the Consumer Financial Protection Bureau. The abrupt resignation comes days ahead of hearings before the Senate Select Intelligence Committee and House Select Intelligence Committee over the Obama administration’s handling of Benghazi.

Six weeks following the assault on a U.S. diplomatic outpost in Libya, many questions remain regarding the nature of the attacks, what the Obama administration knew and when, and the way that knowledge was delivered to the public. Adding to that confusion is the GOP’s desire to politicize the issue in the run-up to the presidential election.

Mitt Romney was widely scorned for criticizing Obama in the assault’s immediate aftermath for allegedly sympathizing with the attackers. But days later, Romney, his allies and other pundits found an opening to again criticize the administration. U.N. Ambassador Susan Rice claimed that the attack in Libya was an outgrowth of the protests in Cairo against an anti-Muslim film. But the administration’s story soon changed.

This shift in story — while always likely given the nature of intelligence — launched a new round of condemnation against Obama. Accusations and speculation of administration lies and cover-ups have been the major focus of the narrative since then.

But the reality is much more nuanced than what the built-up narrative suggests. The following is a timeline of not the attack itself, but the response to it, by the Obama administration, Mitt Romney’s campaign and the right-wing:

THE IMMEDIATE AFTERMATH

September 11, 2012: Protests take place at the U.S. embassy in Cairo. The anger was reportedly sparked by a video, purported to be the trailer of a full-length movie, called “The Innocence of Muslims,” that portrayed Islam in a highly negative and derogatory light. This demonstration will soon spread to other cities throughout the Middle East, including Khartoum, Sanaa and Tunis.

September 11: Dozens of armed militants launch an attack on an American diplomatic outpost in the Libyan city Benghazi.

September 11: Governor Mitt Romney’s campaign issues a statement condemning the Obama administration’s response to the global protests:

ROMNEY: “I’m outraged by the attacks on American diplomatic missions in Libya and Egypt and by the death of an American consulate worker in Benghazi. It’s disgraceful that the Obama administration’s first response was not to condemn attacks on our diplomatic missions, but to sympathize with those who waged the attacks.”

September 12: Initial reports surface that Ambassador Chris Stevens has been killed, along with other American citizens. The story of how continues to shift throughout day as details emerge.

September 12: In the immediate aftermath of news of Ambassador Stevens’ death, Republicans criticized the Romney campaign’s statement. But the campaign stuck to its attack. When asked about the statement, Romney foreign policy advisor Richard Williamson, replied, “It was accurate.”

September 12: The New York Times reports that “[f]ighters involved in the assault…said in interviews during the battle that they were moved to attack the mission by anger over a 14-minute, American-made video that depicted the Prophet Muhammad, Islam’s founder, as a villainous, homosexual and child-molesting buffoon.” The Times continues to stand by its story.

September 12: President Obama and Secretary of State Hillary Clinton give remarks on the death of Ambassador Stevens and others. Both pledge justice against the perpetrators of the attacks. In his speech, Obama refers to the attack as an “act of terror”:

OBAMA: No acts of terror will ever shake the resolve of this great nation, alter that character, or eclipse the light of the values that we stand for. Today we mourn four more Americans who represent the very best of the United States of America. We will not waver in our commitment to see that justice is done for this terrible act. And make no mistake, justice will be done.

September 13: White House Press Secretary Jay Carney says during a press briefing and a later press gaggle that the protests around the world were due to reaction to the video. In the gaggle, Carney made clear he didn’t want to speculate in light of the ongoing investigation. His remarks were later taken to mean that the Benghazi attack was based on video.

September 13: President Obama, at a campaign rally in Denver, CO, reiterates the previous day’s statement, referring to the events in Benghazi as an act of terror:

OBAMA: So what I want all of you to know is that we are going to bring those who killed our fellow Americans to justice. I want people around the world to hear me: To all those who would do us harm, no act of terror will go unpunished. It will not dim the light of the values that we proudly present to the rest of the world. No act of violence shakes the resolve of the United States of America.

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Chairman of the Joint Chiefs of Staff Gen. Martin Dempsey urged against an Israeli strike on Iran’s nuclear program, telling CNN’s Fareed Zakaria this morning that “It’s not prudent at this point to decide to attack Iran,” and such a strike would be “destabilizing and wouldn’t achieve [Israel's] long-term objectives.”

Dempsey, the highest ranking military officer in the U.S., went on to emphasize that while all options remain on the table, U.S. intelligence indicates that Iran has not yet decided to pursue a nuclear weapon:

MARTIN DEMPSEY: We also know, or believe we know, that the Iranian regime has not decided that they will embark on the [...] effort to weaponize their nuclear capability.

FAREED ZAKARIA: You think that is still unclear? [...]

DEMPSEY: It is. I believe it is unclear and on that basis I think it would be premature to exclusively decide that the time for a military option was upon us.

Watch the interview:

Dempsey’s conclusion that Iran has not yet decided to pursue a nuclear weapon reflects the consensus view of the U.S. intelligence community and the IAEA. Director of National Intelligence James Clapper told the Senate Armed Service Committee on Thursday that Iran’s leadership had not yet decided to develop a nuclear weapon but were “keeping themselves in a position to make that decision.”

The November IAEA report on Iran’s nuclear program found that while there were possible military dimensions to Iran’s nuclear program, the nuclear watchdog agency couldn’t confirm that Tehran was pursuing a nuclear weapon. The IAEA’s findings were upheld by CIA Director David Petraeus last month. Petraeus told the Senate Intelligence Committee that the IAEA report is “the authoritative document” on Iran’s nuclear program.

Indeed, a nuclear weapons possessing Iran would be destabilizing but while hawks on Capitol Hill are eager to portray Iran as a “martyr state” hellbent on acquiring nuclear weapons, senior intelligence and military officials take a very different view. “We are of the opinion that the Iranian regime is a rational actor,” said Dempsey. “And it’s for that reason that we think the current path we’re on is the most prudent path at this point.”

Despite efforts from congressional hawks like Sens. Lindsey Graham (R-SC), Joe Lieberman (I-CT) and John McCain (R-AZ), Senate Democrats are resisting efforts to limit President Obama’s policy options on Iran.

The hawkish Senators’ lack of success is noticeable as the three men are seen as as some of the most influential Senators on foreign policy and national security. But their efforts to roll out a piece of bipartisan legislation pressuring the White House’s hand on diplomacy with Iran has found few allies across the aisle. Sens. Bob Casey Jr. (D-PA) reportedly signed onto the legislation and Sen. Richard Blumenthal (D-CT) is rumored to be on board. But Senate Democrats are concerned that the resolution “would be seen as creeping toward an authorization of military force against Iran,” reports The Hill’s Alexander Bolton.

A Senate aid denied that characterization of the legislation and emphasized that it is not an authorization of military action and leaves the option of further negotiations.

However a statement last month from Graham and Lieberman stated, in no uncertain terms, that they would support a bipartisan resolution explicitly opposing containment. The statement read:

When it comes to addressing the threat of a nuclear-armed Iran, all options must be on the table — except for one, and that is containment. [...] Containment is failure, and failure cannot be an option.

Neither U.S. intelligence officials nor the IAEA have concluded that Iran has decided to pursue a nuclear weapon.

Indeed the IAEA has stated concerns about possible military dimensions to Iran’s nuclear program but senior U.S. intelligence officials have expressed support for ongoing sanctions and diplomacy.

Efforts to press Obama to employ the “military option” continue to be discussed in Washington but the partisan divide between those urging action — be it in Congress or outside pressure groups — and those pursuing diplomacy and sanctions is becoming increasingly distinct as Republicans seek to portray the President as weak on national defense and foreign policy.

The past week brought heightened discussion of a potential Israeli unilateral attack on Iran’s nuclear facilities. But House Intelligence Chairman Rep. Mike Rogers (R-MI), appearing on CNN’s State of the Union with Candy Crowley this morning, agreed that an Israeli attack would “light the Middle East on Fire” and could be “a real problem for the national security interests of the United States.”

Rogers, commenting on Washington Post columnist David Ignatius’ report that Defense Secretary Leon Panetta believes “there is a strong likelihood that Israel will strike Iran in April, May or June,” told Crowley:

MIKE ROGERS: [...] My argument is this is too important for us not to get this right. If Israel does a unilateral strike this could be a real problem for the national security interests of the United States.

CANDY CROWLEY: Well it lights the Middle East on fire basically.

ROGERS: Absolutely.

Rogers defended diplomatic and economic efforts to persuade Iran to cooperate fully with U.N. nuclear inspectors:

ROGERS: [The sanctions] seem to be working. The financial pressure right now on Iran is devastating. [...] It’s effecting every sector of their economy. [...] Our argument is can we work with the Israelis on this and other programs to try to delay or stop this program by bringing Iran to the table. That to me is a better outcome than inflaming the Middle East.

Watch it:

Rogers is not alone in voicing misgivings about an Israeli unilateral attack. In January, George W. Bush’s CIA Director Gen. Michael Hayden disclosed that the Bush administration concluded that attacking Iran “would guarantee that which we are trying to prevent — an Iran that will spare nothing to build a nuclear weapon.” Speaking last June, retired Israeli spy chief Meir Dagan warned that an Israeli attack on Iran was “the stupidest thing I have ever heard” and the fallout from such an attack would pose an “unbearable” security challenge. A recent Council on Foreign Relations report highlighted one of the immediate consequences of a military escalation with Iran: a sudden oil price shock (about $23 per barrel in the first days) following an Israeli strike.

Last week, retired Israeli Lt. Gen. Amnon Lipkin-Shahak told The Independent that the IDF leadership doesn’t support military action at this point and Panetta told reporters, “Israel has indicated they are considering this, and we have indicated our concerns.”

Rogers’ worries about blowback from an Israeli strike may also be shared by Israel’s new air force chief, Maj. Gen. Amir Eshel. The Associated Press reports that Eshel is “less enthusiastic about a possible attack on Iran” than outgoing air force chief Maj. Gen. Ido Nehushtan.

Last November, the U.N. nuclear watchdog the International Atomic Energy Agency reported that Iran has engaged in nuclear activity that is “specific to nuclear weapons.” While an Obama administration official noted that the report “does not assert that Iran has resumed a full scale nuclear weapons program,” the IAEA’s director general has repeatedly reiterated, in order to “alert the world,” that Iran’s nuclear program “suggests the development of nuclear weapons.”

Director of National Intelligence James Clapper told the Senate Intelligence Committee today that Iran has not decided on whether it will go forward with building nuclear weapons, and CIA Director David Petraeus concurred with that assertion. When Sen. Diane Feinstein (D-CA) said during the hearing that the IAEA “must make transparent and public what they find” in Iran, Petraeus pointed to nuclear watchdog’s November report, calling it “the authoritative document” on Iran’s nuclear program:

PETRAEUS: The IAEA inspectors are in Iran right now. I believe their past report was a very accurate reflection of reality, of the situation on the ground. I think that is the authoritative document when it comes to informing the public of all the countries of the world of the situation there. Iran is supposedly, reportedly trying to be more open this particular time perhaps trying to reassure countries as it feels the increased bite of the new sanctions, of the Central Bank of Iran sanctions and the reduction in the purchase of oil from some of its key customers and so I look forward, as do others, to seeing what that public report will provide this time believing again that it will be again the authoritative open source document on the program that Iran is pursuing in the nuclear field.

Watch the clip:

IAEA inspectors were just in Iran getting clarification about concerns it has regarding nuclear weapons related activities and will report their findings to the director general.

In the confrontational, climactic scene of the the classic 1964 Cold War film Seven Days in May, President Jordan Lyman barks a question in frustration at Gen. James Mattoon Scott, the leader of a right-wing military conspiracy to overthrow the U.S. government. “Why in the name of God don’t you have any faith in the system of government you’re so hell-bent to protect?” says the president, slamming his hand on the table. A much toned down version of this drama plays out today, too. Only now it’s the generals — the top brass, no less — using strong language to remind politicians of the delicacies of the American republic.

Perhaps taking their cues from Congress or neocon websites, GOP presidential candidates long ago settled on a battle cry against President Obama’s national security record: the almost universal theme that the President should do to what the generals tell him. Texas governor Rick Perry said it about Afghanistan and Iraq. Rep. Michele Bachmann (R-MN) said it about reinstating Don’t Ask Don’t Tell (many generals were for the repeal). Former Massachusetts governor Mitt Romney said he would do what the generals want on Afghanistan, before backing down. Former House speaker Newt Gingrich went the other way, reversing his support for civilian control in favor of wondering why Obama “overrule(d) all his generals.”

But during a press availability while traveling in Saudia Arabia, the top U.S. military officer sang a different tune, using harsh language to describe the talking point about deferring national security and war decisions to the generals. Asked about the line, Gen. Martin Dempsey, the Chairman of the Joint Chiefs of Staff, said:

I’ll probably make news with this but I find some of those articles about divergence or control of the generals to be kind of offensive to me.

And here’s why. One of the things that makes us as a military profession in a democracy is civilian rule. Our civilian leaders are under no obligation to accept our advice; and that’s what it is. Its advice. It’s military judgments, it’s alternatives, it’s options. And at the end of the day, our system is built on the fact that it will be our civilian leaders who make that decision and I don’t find that in any way to challenge my manhood, nor my position. In fact, if it were the opposite, I think we should all be concerned.

Dempsey isn’t the first top military officer to tell politicians about the chain-of-command recently. This summer, the last two Joint Chiefs chairmen, Gen. David Petraeus, since retired and leading the CIA, and the now-retired Admiral Michael Mullen, explained the concept in hearings on Capitol Hill.

At a time of continuing economic crisis in the U.S. and around the world, President Obama’s administration has amassed a record of successes in national security. Irrespective of controversies over some of the policies, Obama has pursued perceived threats in a broadened, borderless drone war; engaged in a NATO war to protect civilians in Libya; and is on the verge of ending one ground war and planning to wind down another even longer one. But this is just not good enough for some conservatives, who insist on portraying Obama as a stereotypical lily-livered liberal afraid to indefinitely continue large-scale U.S. military commitments abroad. The chosen line of attack relies on the now-commonplace trope that Obama doesn’t listen to his generals when formulating his security strategies.

The latest salvo in this assault comes from neoconservative legacy Fred Kagan, a fellow at the American Enterprise Institute (AEI). Kagan concludes a Weekly Standard piece — “The President & the Generals” — by writing:

Under no circumstances should the president of the United States ever take an important military decision simply because a uniformed officer has recommended it. But, when the president does overrule his commanders, he had better have an extremely good reason not only to reject their advice but to prefer his own wisdom. And if he finds himself doing it repeatedly, he would do well to consider what the source of the problem really is.

Given most of the Republican presidential field’s shaky understanding of civilian control of the military, Kagan’s “under no circumstances” caveat is welcome. Nonetheless, Kagan’s implication here is obvious: the real “source of the problem” is Obama himself. Kagan, then, would do well consider for himself that there’s been another overarching problem affecting government decisions over the past three years: a financial crisis of epic proportions that has, is, and will likely continue to bear on decisions made by a commander-in-chief, though, crucially, not on commanders on the ground. And while military commanders are charged with making tactical recommendations and informing on military strategy, the president decides the country’s overall national security strategy, a concept Kagan seems to have overlooked.

Retired Gen. David Petraeus, who, in 2010, won AEI’s prestigious Kristol Award, hinted at such disparity between the purviews of a president and his generals when he explained the chain-of-command at a confirmation hearing to his current post atop the Central Intelligence Agency. Petraeus, at the time the top U.S. military officer for Afghanistan, said:

[A]t every level of the chain of command above me there are additional considerations, and each person above me, all the way up to and including the president has a broader purview and broader considerations that are brought to bear. The president alone [is] in the position of evaluating all those different considerations, including certainly those of the commander on the ground but also many others as well in reaching his decision.

Petraeus lamented that he wasn’t getting everything he wanted from a military standpoint, but acknowledged that he was “talking about small differences” and that the situation was “understandable in the sense that there are broader considerations beyond just those of a military commander.” He went on to say that no military commander gets everything they want:

The fact is that there has never been a military commander in history who has had all the forces he would like to have. Or all the time. Or all the money. Or all the authorities. Or, nowadays, all the bandwidth.

So, if Obama “finds himself [making different decisions than his generals] repeatedly,” that isn’t quite the extraordinary situation Kagan posits.