The strongest pushback against President Trump came instead from a source never contemplated by the founders: his own branch of the government. The F.B.I. and the intelligence agencies opened their investigations of Russian interference in the 2016 election even before Mr. Trump took the oath of office. The president thought that he could quash this inquiry by dismissing James Comey, the F.B.I. director, but as the president’s strategist Steve Bannon reportedly cautioned, “you can’t fire the F.B.I.” Mr. Trump’s appointee as deputy attorney general, Rod Rosenstein, initiated the special counsel inquiry and appointed Mr. Mueller to lead it, while Attorney General Jeff Sessions — an early Trump backer — refused to “unrecuse” himself from the Russia investigation.

Even more surprising, resistance arose from key White House personnel. In June 2017, when Mr. Trump tried to remove Mr. Mueller, the White House counsel Donald McGahn refused to carry out the directive. The next month, when Trump tried to get Mr. Sessions to limit the special counsel’s jurisdiction, the White House deputy chief of staff, Rick Dearborn, declined to relay the order to the attorney general. Later in July 2017, when Mr. Trump told White House chief of staff Reince Priebus to demand Mr. Sessions’s resignation, Mr. Priebus refused. Mr. McGahn also disobeyed the president’s early 2018 directive to create a false paper trail obscuring an earlier effort by Mr. Trump to have the special counsel fired.