Chief of Staff John Kelly wanted to know, after revelations had surfaced that Pruitt had been renting living space in Washington, D.C., from a pair of high-powered lobbyists—one of whom was lobbying his agency at the time—what other shoes, if any, were going to drop. Is there anything else that “hasn’t come out” yet, Kelly asked, according to three Trump administration sources. The chief of staff then impressed upon Pruitt that, though he has the full public confidence of President Trump for now, the flow of negative and damning stories needed to stop soon, as one source briefed on the contents of the call described…

Shortly thereafter, The Atlantic reported that Pruitt had defied the White House and directed his staff to give raises to a pair of employees under an obscure provision of the Safe Drinking Water Act, which gives the administrator wide latitude over short-term staffing decisions prompted by an emergency or other unexpected development. (Pruitt denied any knowledge of the raises in an interview with Fox News on Wednesday afternoon.)

According to two sources with knowledge of the situation, Kelly and other senior White House officials were blindsided by major details in The Atlantic’s article, left frustrated and wondering if Pruitt and the EPA still weren’t conveying damaging news to the West Wing.