Holding his first news conference since mid-July, President Obama fielded questions today about Islam and national security as issues of religious tolerance and America's two wars in the Muslim world have fed controversies over the past month.

Obama spent a good portion of it offering passionate defenses of Islam and religious equality, while urging Americans to see the fight against terrorism as just that--a war on specific al Qaeda terrorists--and not as a cultural or religious war against Islam.

"One of the things that I most admired about President Bush is, after 9/11, him being crystal clear about the fact that we were not at war with Islam, we were at war with terrorists and murderers who had perverted Islam, who had stolen its banner to carry out outrageous acts," Obama said. "I want to make sure that this country retains that sense of purpose [of religious equality], and I think tomorrow is a wonderful day for us to remind ourselves of that."

The nation's attention has been captivated, somehow, over the past few days by lone Florida pastor Terry Jones and his plan to burn copies of the Koran this weekend in connection with the ninth anniversary of the 9/11 attacks. Obama had previously condemned the plan, and Defense Secretary Robert Gates phoned Jones to attempt to dissuade him. Today in Kabul, news of Jones's plan led to violent protests.

Obama responded to a question about Jones by reiterating his opposition to the plan:

Let me repeat what I said a couple of days ago: The idea that we would burn the sacred texts of someone else's religion is contrary to what this country stands for. It's contrary to what this nation was founded on, and my hope is that this individual prays on it and refrains from doing it. 

Addressing whether his administration had elevated Jones unnecessarily by having its defense secretary call him, Obama stressed that Jones' plans have threatened the safety of U.S. troops while subtly noting that the media, not the administration, have fed Jones with attention:

But I'm also commander in chief, and we are seeing today riots in Kabul, riots in Afghan, that threatened our young men and women in uniform, and so we've got an obligation to send a very clear message that this kind of behavior or threats of action put our young men and women in harm's way, and it's also the best imaginable recruiting tool for al Qaeda, and though this may be one individual in Florida, it is my concern that we don't have a whole bunch of folks across the country thinking that this is the way to get attention. This is endangering our troops, endangering our sons and daughters.

... you don't play games with that. So I hardly think we're the ones who elevated this story, but it is, in the age of the Internet, something that can cause us profound damage around the world, and so we've gotta take it seriously.

On the so-called "Ground Zero mosque," another controversial topic from the past month, Obama offered a full-throated endorsement of Muslims' constitutional right to build it, but he also went a step further, suggesting that it's offensive to try to dissuade them from doing so.

"When we start acting as if their religion is somehow offensive, what are we saying to them?" Obama said. (See his full remarks on the topic here.)

Asked about the war in Afghanistan, President Obama sought to remind viewers why the U.S. invaded the country in the first place: "We're there because that was the place where al Qaeda launched an attack that killed 3,000 Americans, and we want to make sure that we dismantle al Qaeda and that Afghanistan is never again used as a base for attacks against Americans and the American homeland," Obama said while acknowledging that the administration is "in the midst of a very difficult but very important project" in trying to establish Afghan President Hamid Karzai's government as a credible, non-corrupt governance system and a reliable security force for Afghanistan.

America is doing better the war against terrorism now than it has in past years, Obama said, telling reporters that the administration has succeeded in "ramp[ing] up the pressure on al Qaeda and their leaders, who "have been holed up in ways that makes it harder for them to operate."

The threat of terrorism is basically ongoing, Obama said when asked if he sees an end to it. But that doesn't mean Americans should live in fear or fundamentally chance, he said.

"I think that in this day and age, there is always going to be the potential for an individual or a small group of individuals, if they are willing to die, to kill other people," Obama said.

The president admitted that his administration has failed to make good on his campaign promise of closing Guantanamo, and he admitted that Congress retains a critical measure of control over the planned closure, which stalled after efforts to deny funding gained momentum in Congress.

"We're going to work with members of Congress, and this is going to have to be on a bipartisan basis to move this forward," Obama said.

Tomorrow will mark President Obama's second 9/11 anniversary in office. Last year, he identified it as a "national day of service," partly, it seems, to incorporate a positive element into a day marked by anger, fear, and sorrow. Obama made brief reference to the national day of service in his remarks today.

We want to hear what you think about this article. Submit a letter to the editor or write to letters@theatlantic.com.