CTL, the Judicial Branch is NOT part of the Executive Branch, and contrary to your comment I said nothing about the President ordering any Judicial Branch member to do anything. The Executive, Judicial and Congressional branches are the three independent, of each other, branches of the United States government.
And the President legally CAN directly order the FBI chief and the FBI to open or close any investigation. He can also order a US Attorney to prosecute or not prosecute a case.