FORTUNE — Since Fortune published “The Truth about the Fast and Furious Scandal” on June 27, thousands of comments have been posted on Fortune.com either praising or vilifying the article. Among the questions often raised by critics of the article (including Sen. Charles Grassley) concern assertions that the ATF encouraged gun dealers to sell weapons to known traffickers. If the ATF was encouraging such sales, the argument goes, it would be proof that the agency had a policy to allow weapons to fall into the hands of Mexican drug cartels, the core contention in what is known as the Fast and Furious scandal.

In the six months of investigations that led Fortune to conclude that the ATF had no policy to intentionally permit weapons to be trafficked, we examined 2,000 pages of ATF records, Congressional reports and testimony, and interviewed 39 people involved in or knowledgeable about the case. That body of evidence shows the ATF did not have a policy of encouraging gun dealers to sell to traffickers. Until now, the alleged encouragement of gun-dealers has not been a central focus of the Fast and Furious scandal. As a result, we did not address those points in the article. However, given the interest in this question, we thought it was worth taking readers through the evidence on this point.

It should be noted at the outset that the Congressional committee investigating Fast and Furious has never claimed the ATF had any official, written policy to encourage gun dealers to sell to traffickers. No documents, emails, or testimony mentioned in Congressional reports show signs of an agency-wide policy, or even a policy within Phoenix Group VII, the unit that worked on Fast and Furious.

What the allegations in the Congressional hearings and reports boil down to are two specific situations. In one, as we’ll see, the allegations are true — but misleading and incomplete — and in the second, the evidence is contradictory. It’s possible that the Congressional investigators have other evidence, but these two episodes are the only ones that have surfaced to date.

Claim No. 1

In August 2010, after a successful wiretap led Phoenix Group VII to seize 114 weapons in a single month, an employee at a gun dealership informed Group VII supervisor Dave Voth that one of their chief suspects was looking to purchase 20 9mm pistols. Based on evidence it had gathered on the wiretap, the ATF had enough probable cause to immediately arrest the suspect if he purchased the weapons. So — in the only such instance known to date — Voth wrote back and asked the dealer to make this particular sale. Voth says he encouraged the sale so that the agents could arrest the suspect outside the gun dealership. In the end, however, the suspect did not make the purchase and the arrest did not take place. No evidence has emerged that Voth ever made such a statement to any other gun seller.

Claim No. 2

This allegation involves a gun store called Lone Wolf Trading Company and shifting assertions made by its owner, Andre Howard. ATF records and Justice Department correspondence show that Voth and federal prosecutor Emory Hurley met with Howard soon after Voth arrived in Arizona. According to those records, Hurley advised Howard that, obviously, he could not make illegal sales (which he wasn’t), and needed to use his judgment regarding legal sales, but that the government would appreciate any information about the purchasers and the sales to aid the investigation. Lone Wolf cooperated with the ATF, according to agency documents, regularly providing records of gun sales and permitting the ATF to install a surveillance camera in the store.

Lone Wolf was in a sensitive position. From 2006 to 2011, it was the No. 1 seller in Arizona of weapons that were later found at Mexican crime scenes, according to ATF data. The store, which had been prominently mentioned in a Washington Post article on indiscriminate firearms sales, also sold the weapons found at the murder scene of U.S. Border Patrol agent Brian Terry. On Feb. 1, 2011, six weeks after Terry’s death, Howard released a press statement that defended the ATF: “These federal agencies,” it noted, “conduct themselves in a very professional and proper manner…. Senator Grassley’s office contacted us regarding ‘any’ impropriety by ATF and we have stated that their [sic] exists no indication to that effect.” Howard went on to conclude that people should “stop pointing blame at either Federal or state agencies attempting to do their job” and instead “give them the tools to accomplish this monumental problem confronting them.”

However, as the scandal heated up and the ATF was deluged with criticism, Howard revised his account and directed the blame at the agency. In September 2011, he told the Los Angeles Times that he was directed by ATF to sell guns — as many as possible, regardless of the legality, and that selling so many guns made him feel “horrible and sick.” This contention is the second element that backs the claim that the ATF encouraged gun dealers to sell to traffickers.

Fortune visited Lone Wolf in January and requested an interview. The owner declined, but denounced the ATF, accused its agents of murder, and said answers would more likely be found on Constitution Avenue, the address of the Justice Department in Washington, D.C.

The totality of the evidence — including the ATF and Justice Department documents that directly contradict Howard’s revised position, and his own earlier defense of ATF — undermines his subsequent claims. And neither the Lone Wolf case, nor the one episode in which Voth encouraged a gun sale in the hopes of making an arrest in the parking lot of the store right after the sale, support the assertion that the ATF had a policy to intentionally permit gun-trafficking to Mexico.

Note: An earlier version of this story incorrectly described the 9mm guns as “cop killer.”