On May 14, 2007, after a Muslim terror plot was uncovered at Fort Dix in New Jersey, Times reporter Alan Feuer ignored clear evidence  to claim: "It is unclear what role, if any, religion played in the attack Mr. Shnewer and the five other men are charged with planning." A May 26, 2009  Times story on synagogue bombing plots in The Bronx also denied the obvious: "In fact, it is uncertain just how much of a role their faith played in their motivation."
Perhaps the most offensive passage from the paper's Fort Hood coverage was when White House reporter Sheryl Gay Stolberg bizarrely pondered, in a story filed Saturday that didn't make the print edition, what the massacre meant for President Obama - "Obama Offers Sympathy and Urges No 'Jump to Conclusions.' "
Mr. Obama has made it a goal of his presidency to repair relations with Muslims around the world; in a major speech in Cairo this year, he called for a "new beginning" with the Muslim world. The shootings at Fort Hood, however, pose a different problem for the president, by shining a spotlight on the tensions Muslims can feel inside the United States.
The paper's speculation about Major Nidal Malik Hasan's motives trod familiar liberal anti-war paths, including raising the ideas of general "tensions," combat stress, and anti-Muslim discrimination, as in Monday's front-page story, "After Years of Growing Tensions, 7 Minutes of Bloodshed " from Killeen, Texas by James McKinley Jr and James Dao:
...[Nasan] bowed his head for several seconds, as if praying, stood up and drew a high-powered pistol. "Allahu akbar," he said - "God is great." And he opened fire. Within minutes he had killed 13 people.
But relatives and acquaintances say tensions that led to the rampage had been building for a long time. Investigators say Major Hasan bought the gun used in the massacre last summer, days after arriving at Fort Hood.
In recent years, he had grown more and more vocal about his opposition to the wars in Iraq and Afghanistan and tortured over reconciling his military duties with his religion. He tried to get out of the Army, relatives said, and apparently believed it to be impossible, though experts say he was probably given inadequate advice.
At times, he complained, too, about harassment, once describing how someone had put a diaper in his car, saying, "That's your headdress." In another case cited by relatives, someone had drawn a camel on his car and written under it, "Camel jockey, get out!"
The Times did outline Hasan's strict Muslim views, rejecting women at his mosque because he did not "find any of them pious enough" and relayed his conversation with a friend, Duane Reasoner, in which he allegedly said: "In the Koran, it says you are not supposed to have alliances with Jews or Christians, and if you are killed in the military fighting against Muslims, you will go to hell."
Andrea Elliott, who won a Pulitzer Prize in 2007 for a series of blandished profiles of Muslim imams in New York City, wrote "Complications Grow for Muslims Serving Nation " for Monday's edition:
Abdi Akgun joined the Marines in August of 2000, fresh out of high school and eager to serve his country. As a Muslim, the attacks of Sept. 11 only steeled his resolve to fight terrorism.
But two years later, when Mr. Akgun was deployed to Iraq with the 26th Marine Expeditionary Unit, the thought of confronting Muslims in battle gave him pause.
He was haunted by the possibility that he might end up killing innocent civilians.
Elliott downplayed Hasan's radical motivations:
It is unclear what might have motivated Major Hasan, who is suspected of killing 13 people. Senior military and law enforcement officials said they had tentatively dismissed the possibility that he was carrying out a terrorist plot. He seems to have been influenced by a mixture of political, religious and psychological factors, the officials said.
Muslim leaders, advocates and military service members have taken pains to denounce the shooting and distance themselves from Major Hasan. They make the point that his violence is no more representative of them than it is of other groups to which he belongs, including Army psychiatrists.
Elliott singled out anti-Muslim taunts, as if that was some kind of justification, and Abu Ghraib of course came in for blame:
"In the Koran it says that war is to end the state of oppression and to uplift the oppressed," said Khaled Abou El Fadl, a professor at the law school at the University of California, Los Angeles.
But he and others interviewed said it has been increasingly difficult for Muslims to support the wars in Iraq and Afghanistan, as accounts have emerged of the killing of civilians, the corruption of American-backed local governments, and prisoner abuses like that of the Abu Ghraib scandal.
And Sunday's front-page story by Benedict Carey, Damien Cave, and Lizette Alvarez, "A Military Therapist's World: Long Hours, Filled With Pain ," suggested Hasan may have snapped "partly under the stress of the job and impending deployment."
Many of the patients who fill the day are bereft, angry, broken. Their experiences are gruesome, their distress lasting and the process of recovery exhausting. The repeated stories of battle and loss can leave the most professional therapist numb or angry.
And hanging over it all, for psychiatrists and psychologists in today's military, is the prospect of their own deployment - of working under fire in Iraq or Afghanistan, where the Pentagon has assigned more therapists to combat units than in previous wars.
That was the world that Maj. Nidal Malik Hasan, an Army psychiatrist, inhabited until Thursday, when he was accused of one of the worst mass shootings ever on a military base in the United States, an attack that killed 13 and left dozens wounded. Five of the dead were fellow therapists, the Army said.
If it turns out that Major Hasan did in fact break partly under the stress of the job and impending deployment, many veterans would not be surprised.