Bill Keller

Bush Administration Keller and The Times also published a story on another classified program to monitor terrorist-related financial transactions through the Brussels, Belgium-based Society for Worldwide Interbank Financial Telecommunication (SWIFT) on June 23, 2006. Many commentators, as well as some elected officials such as U.S. Congressman Peter T. King, called for the U.S. Justice Department to prosecute The New York Times and the confidential sources who leaked the existence of this counter-terrorism program despite relevant statutes that forbid revealing classified information that could threaten national security, especially in a time of war.

In an attempt to respond to criticism stemming from the disclosure of the classified Terrorist Finance Tracking Program, the NSA program's official name, Keller stated in a published letter that President Bush himself had acknowledged as early as September 2001 that efforts were underway "to identify and investigate the financial infrastructure of the international terrorist networks" and "to follow the money as a trail to the terrorists." In an Op-ed column in The Times, Keller, together with Los Angeles Times editor Dean Baquet wrote that "Our job, especially in times like these, is to bring our readers information that will enable them to judge how well their elected leaders are fighting on their behalf and at what price." Keller's critics, including U.S. Treasury Secretary John W. Snow, responded to Keller's letter by pointing out that there is a vast difference between stating general intentions to track terrorist finances and the exact means employed to achieve those goals. But, as Keller wrote, this was the same Secretary Snow who invited a group of reporters to a 6-day trip on a military aircraft "to show off the department's efforts to track terrorist financing."

Keller was a leading supporter of the 2003 invasion of Iraq, explaining his backing for military action in his article 'The I-Can't-Believe-I'm-A-Hawk Club'. Two days after the invasion, Keller wrote the column 'Why Colin Powell Should Go', arguing for US Secretary of State's resignation because his strategy of diplomacy at the UN had failed. In contrast, Keller was much more sympathetic to Deputy Defence Secretary Paul Wolfowitz, describing him as the 'Sunshine Warrior'.

On July 6, 2005, Keller spoke in defense of Judith Miller and her refusal to give up documents relating to the Valerie Plame case.

NSA Terrorist Surveillance Program

Keller was reported to have refused to answer questions from The Times public editor, Byron Calame, on the timing of the December 16, 2005, article on the classified National Security Agency (NSA) Terrorist Surveillance Program. Keller's delay of the paper's reporting about NSA overreach until after Bush's close reelection was controversial. The Times's series of articles on this topic won a Pulitzer Prize. The source of the disclosure of this NSA program was investigated by the United States Justice Department. The NSA program itself was reviewed by the Senate Judiciary Committee as to whether it sidesteps the Foreign Intelligence Surveillance Act, and after The Times articles, the Administration changed its procedures, allowing for more safeguards and more Congressional and judicial oversight.

Keller discussed the deliberations behind the Times decision to publish the story on July 5, 2006, in a PBS interview with Jeffrey Brown that included a discussion of the issues involved with former National Security Agency Director Admiral Bobby Ray Inman.

Catholic Church sex abuse crisis

Keller widely reported on the Catholic sex abuse cases and flatly put the blame on John Paul II himself : "The uncomfortable and largely unspoken truth is that the current turmoil in the Roman Catholic Church is not just a sad footnote to the life of a beloved figure. This is a crisis of the pope's making."

Nelson Mandela

Keller wrote a 128-page juvenile biography of Nelson Mandela published by Kingfisher Books in 2008, Tree Shaker: The Story of Nelson Mandela. He had served as the Times bureau chief in Johannesburg from April 1992 to May 1995 In February 2014, The New York Times reported that Keller was going to work for the Marshall Project. The Marshall Project formally launched in November 2014. Keller was editor in chief of the Marshall Project from 2014 until his retirement in 2019.