Political activity
In 1999, Democratic U.S. Attorney General Janet Reno appointed Danforth to lead an investigation into the FBI's role in the 1993 Waco Siege. Danforth appointed Democratic U.S. Attorney Edward L. Dowd Jr. for the Eastern District of Missouri as his deputy special counsel. He also hired Bryan Cave partner Thomas A. Schweich as his chief of staff. Assistant U.S. Attorney James G. Martin served as Danforth's director of investigative operations for what became known as the "Waco Investigation" and its resulting "Danforth Report".
In July 2000, Danforth's name was leaked as being on the short list of potential vice presidential nominees for Republican nominee George W. Bush, along with Michigan Governor John Engler, New York Governor George Pataki, Pennsylvania Governor Tom Ridge, and former U.S. Secretary of Transportation, U.S. Secretary of Labor and former American Red Cross President Elizabeth Dole. One week before the 2000 Republican National Convention was held in Philadelphia, campaign sources said that Dick Cheney, the man charged with leading the selection process for the nominee, had recommended Danforth. But Danforth wanted to continue living mainly in Missouri, where his family was still based, and formally declined to run for vice president on July 11, 2000. Bush ultimately selected Cheney himself. Bush wrote in his book Decision Points that Danforth would have been his choice if Cheney had not accepted; on July 28, 2000, The New York Times reported that the choice of Cheney as Bush's running mate was secretly made "weeks" before it was formally announced on July 25. On September 6, 2001, Bush appointed Danforth a special envoy to Sudan. He brokered a peace deal that officially ended the civil war in the South between Sudan's Islamic government and the U.S.-backed Christian rebels, but elements of that conflict still remained unresolved (as had the separate Darfur conflict). Known as the Second Sudanese Civil War, the conflict ended in January 2005 with the signing of a peace agreement.
On June 11, 2004, Danforth presided over the funeral of Ronald Reagan, held at Washington National Cathedral. Danforth also officiated at the funerals of Washington Post executive Katharine Graham, former United States Senator Harry Flood Byrd Jr. of Virginia, and Missouri State Auditor Tom Schweich.
On March 30, 2005, Danforth wrote an op-ed in The New York Times critical of the Republican party. The article began: "By a series of recent initiatives, Republicans have transformed our party into the political arm of conservative Christians". He also penned a June 17, 2005, piece headlined "Onward, Moderate Christian Soldiers". At a Log Cabin Republicans meeting on April 30, 2006, Danford publicly expressed opposition to the proposed Federal Marriage Amendment, which would have banned same sex marriages, calling it "silly" and comparing it to Prohibition. In 2015, Danforth and 299 other Republicans signed an amicus brief calling on the Supreme Court to legalize same-sex marriage.
Contributing to the anthology Our American Story (2019), Danforth addressed the possibility of a shared American narrative and focused on the "great American purpose" of "hold[ing] together in one nation a diverse and often contentious people." He encouraged continued work "to demand a functioning government where compromise is the norm, to integrate all our people into one indivisible nation, and to incorporate separated individuals into the wholeness of the community." Danforth is a member of the Reformers Caucus of Issue One.
Danforth was a mentor and political supporter of Josh Hawley, who became Attorney General of Missouri in 2017 and U.S. Senator in 2019 with Danforth's encouragement; Danforth also supported Hawley's presidential ambitions. In the wake of the January 6 United States Capitol attack and Hawley's efforts to challenge the 2021 United States Electoral College vote count, Danforth said that supporting Hawley in the 2018 election "was the worst mistake I ever made in my life". During the 2022 United States Senate election in Missouri, Danforth headed a PAC supporting independent candidate John Wood, considered a long shot to win. Wood collected enough signatures to get on the ballot but dropped out after 50 days when Eric Schmitt won the Republican primary. Danforth spent $6 million on the effort.