On the evening of September 15, CBS aired a segment that featured an interview with Marian Carr Knox, a secretary at Ellington Air Force Base from 1956–1979, and who was Killian's assistant on the dates shown in the documents. Dan Rather prefaced the segment on the recorded interview by stating "She told us she believes what the documents actually say is, exactly, as we reported." In the aired interview, Knox expressed her belief that the documents reflected Killian's "sentiments" about Bush's Service, and that this belief motivated her decision to reach out to CBS to provide the interview. In response to a direct question from Rather about the authenticity of the memo on Bush's alleged insubordination, she stated that no such memo was ever written; she further emphasized that she would have known if such a memo existed, as she had sole responsibility to type Killian's memos in that time period. At this point, she also admitted she had no firsthand knowledge of Bush's time in the Guard. However, controversially, Knox said later in the interview, "The information in here was correct, but it was picked up from the real ones." She went on to say, "I probably typed the information and somebody picked up the information some way or another." The New York Times' headline report on this interview, including the phrase "Fake but Accurate," created an immediate backlash from critics of CBS's broadcast. The conservative-leaning Weekly Standard proceeded to predict the end of CBS's news division.

As media coverage widened and intensified, CBS at first attempted to produce additional evidence to support its claims. On September 11, a CBS News segment stated that document expert Phillip Bouffard thought the documents "could have been prepared on an IBM Selectric Composer typewriter, available at the time." The Selectric Composer was introduced in 1966 for use by typesetting professionals to generate camera-ready copy; according to IBM archives describing this specialized equipment, "To produce copy which can be reproduced with 'justified', or straight left-and right-hand margins, the operator types the copy once and the Composer computes the number of spaces needed to justify the line. As the operator types the copy a second time, the spaces are added automatically.") Bouffard's comments were also cited by the Boston Globe in an article entitled "Authenticity backed on Bush documents." However, the Globe soon printed a retraction regarding the title. CBS noted that although General Hodges was now stating he thought the documents were inauthentic, "we believed General Hodges the first time we spoke with him." CBS reiterated: "we believe the documents to be genuine."

CBS News Producer Mary Mapes obtained the copied documents from Burkett, a former officer in the Texas Army National Guard, while pursuing a story about the George W. Bush military Service controversy. The papers, purportedly made by Bush's commander, the late Lieutenant Colonel Jerry B. Killian, included criticisms of Bush's Service in the Guard during the 1970s. In the 60 Minutes segment, anchor Dan Rather stated: "We are told [the documents] were taken from Lieutenant Colonel Killian’s personal files" and incorrectly asserted that "the material" had been authenticated by experts retained by CBS.

Also on September 10, The Dallas Morning News reported that "the officer named in one memo as exerting pressure to 'sugarcoat' Bush's military record was discharged a year and a half before the memo was written. The paper cited a military record showing that Col. Walter "Buck" Staudt was honorably discharged on March 1, 1972, while the memo cited by CBS as showing that Staudt was interfering with evaluations of Bush was dated August 18, 1973."

Burkett had received publicity in 2000, after making and then retracting a claim that he had been transferred to Panama for refusing "to falsify personnel records of [then-]Governor Bush", and in February 2004, when he claimed to have knowledge of "scrubbing" of Bush's Texas Air National Guard records. Mapes was "by her own account [aware that] many in the press considered Burkett an 'anti-Bush zealot,' his credibility in question."

Some critics of CBS and Dan Rather argued that by proceeding with the story when the documents had not been authenticated, CBS was exhibiting liberal bias and attempting to influence the outcome of the 2004 U.S. Presidential Election. Freelance Journalist Michael Smith had emailed Mapes, asking, "What if there was a person who might have some information that could possibly change the momentum of an election but we needed to get an ASAP book deal to help get us the information?" Mapes replied, "that looks good, hypothetically speaking of course." The Thornburgh-Boccardi report found that Mapes' contact with Kerry adviser Joe Lockhart was "highly inappropriate", and that it "crossed the line as, at a minimum, it gave the appearance of a political bias and could have been perceived as a news organizations' assisting a campaign as opposed to reporting on a story;" however, the Panel did not "find a basis to accuse those who investigated, produced, vetted or aired the Segment of having a political bias." In a later interview with The Washington Post, when asked about the issue of political bias, review panel member Louis Boccardi said "bias is a hard thing to prove." The panel concluded that the problems occurred "primarily because of a rush to air that overwhelmed the proper application of the CBS News Standards".

Some Democratic critics of Bush suggested that the memos were produced by the Bush campaign to discredit the media's reporting on Bush's National Guard Service. The chairman of the Democratic National Committee, Terry McAuliffe, suggested that the memos might have originated with long-time Bush strategist Karl Rove. McAuliffe told reporters on September 10, "I can tell you that nobody at the Democratic National Committee or groups associated with us were involved in any way with these documents," he said. "I'm just saying that I would ask Karl Rove the same question." McAuliffe later pointed out that Rove and another Republican operative, Ralph E. Reed, Jr., had "a known history of dirty tricks," and he asked whether Republican National Committee chairman Ed Gillespie would rule out any involvement by GOP consultant Roger Stone. At a community forum in Utica, New York in 2005, U.S. Representative Maurice Hinchey (D-NY) pointed out that the controversy served Rove's objectives: "Once they did that, then it undermined everything else about Bush's draft dodging. ... That had the effect of taking the whole issue away." After being criticized, Hinchey responded, "I didn't allege I had any facts. I said this is what I believe and take it for what it's worth."

On November 7, 2006, Rather defended the report in a radio interview, and rejected the CBS investigation's findings. In response, CBS spokesman Kevin Tedesco told the Associated Press, "CBS News stands by the report the independent panel issued on this matter and to this day, no one has been able to authenticate the documents in question."

On September 19, 2007, Rather filed a $70 million lawsuit against CBS and its former corporate parent, Viacom, claiming they had made him a "scapegoat" over the controversy caused by the 2004 60 Minutes Wednesday report that featured the Killian documents. The suit names as defendants: CBS and its CEO, Leslie Moonves: Viacom, Sumner Redstone, chairman of both Viacom and CBS Corporation; and Andrew Heyward, the former President of CBS News.

Rove and Stone have denied any involvement. In a 2008 interview in The New Yorker, Stone said "It was nuts to think I had anything to do with those documents...[t]hose papers were potentially devastating to George Bush. You couldn’t put them out there assuming that they would be discredited. You couldn’t have assumed that this would redound to Bush’s benefit. I believe in bank shots, but that one was too big a risk."

On September 29, 2009, New York State Appeals Court dismissed Rather's lawsuit and stated that the lower court should have honored CBS's request to throw out the entire lawsuit instead of just throwing out parts.

The controversy had long-reaching personal, political and legal consequences. In a 2010 issue of TV Guide, Rather's report was ranked #3 on a list of TV's ten biggest "blunders".

Dan Rather continued to stand by the story, and in subsequent interviews stated that he believed that the documents have never conclusively been proven to be forgeries — and that even if the documents are false, the underlying story is true.

The story of the controversy was dramatized in the 2015 film Truth, starring Robert Redford as Dan Rather and Cate Blanchett as Mary Mapes and directed by James Vanderbilt. It is based on Mapes' memoir Truth and Duty: The Press, the President, and the Privilege of Power. The film was, however, not approved by current CBS President and CEO Leslie Moonves. CBS refused to air advertisements for the film and a longtime CBS spokesman stated that "there are (...) too many distortions, evasions and baseless conspiracy theories" [in the movie].