It is the latest effort by President Trump and his allies to impugn the Russia investigation, which the president sees as having been a partisan witch hunt.
The premise of the new inquiry is that classified documents related to the Russia investigation were mishandled at F.B.I. headquarters in downtown Washington, where the director and his senior aides work.
The president focused on cities like Los Angeles and Washington as he deployed federal troops and railed against crime. But on Friday, in reference to San Francisco, he said, “We’ll clean that one up, too.”
San Francisco voters have veered to the middle in recent elections and have chosen more moderate leaders, including their new mayor. Some believed that could be enough to escape President Trump’s attention.
The move appears to diminish the authority of the current deputy director, Dan Bongino, whose tumultuous tenure has included a pitched argument over files related to the disgraced financier Jeffrey Epstein.