Many scholars contend that, George W. Bush’s protestations notwithstanding, the President in many contexts is not the decider regarding federal prosecutions — he’s authorized to appoint and remove deciders, but his job is to supervise.
In 1831, President Andrew Jackson was faced with this very issue. Two years earlier, a man known as Constant Polari or Carrara broke into the palace of Laken [link] in Brussels and stole, among other things, royal jewels belonging to the Prince and Princess of Orange. After some intrigue straight out of National Treasure (some of the items taken were hidden in a compartment in a writing desk), Polari was arrested by U.S. customs agents [link]. Some of the jewels were retrieved, and the President wanted to return them to the Netherlands. Unfortunately, the district attorney was pursuing a forfeiture claim against the jewels and wasn’t inclined to stop. Jackson asked then-attorney general Roger Taney if he could make the DA back off. Taney’s opinion, titled The Jewels of the Princess of Orange [link], said he could, sort of. The President has the power to direct the district attorney to stop, Taney wrote, but:
The District Attorney might refuse to obey the President's order; and if he did refuse, the prosecution, while he remained in office, would still go on; because the President himself could give no order to the court or to the clerk to make any particular entry. He could only act through his subordinate officer, the district attorney, who is responsible to him and who holds his office at his pleasure. And if that officer still continues a prosecution which the President is satisfied ought not to continue, the removal of the disobedient officer and the substitution of one more worthy in his place would enable the President through him faithfully to execute the law.
This advice was put to the test during Andrew Jackson’s Bank War [link]. Jackson opposed the idea of a U.S. central bank, and in 1833 instructed the secretary of the treasury, Louis McLane, to remove the government’s funds from the Second Bank of the United States. Professor Peter Strauss explains [link], “the Bank’s authority ran until 1836, and the relevant statute provided that government funds were to be kept in it ‘unless the Secretary of the Treasury shall at any time otherwise order and direct.’ When Secretary McLane decided against removing the funds, Jackson removed him and appointed William Duane as his successor.” When Duane also said no [link], Jackson appointed Roger Taney to replace him. Taney did as he was told, but that didn’t go over so well with Congress. As Strauss explains:
The Senate passed a Resolution of Censure and subsequently rejected Taney’s nomination as Secretary — the first time in American history it had rejected a presidential nomination to the cabinet. When, in 1835, President Jackson nominated Taney to a seat as Associate Justice of the Supreme Court, that nomination, too, failed. Changes in Senate membership finally permitted his renomination and confirmation as Chief Justice months later, in 1836, and the eventual expungement of the Resolution of Censure.
A more recent example is the the infamous Saturday Night Massacre during the Watergate scandal, when Richard Nixon instructed his subordinates to dismiss the special prosecutor. Both Attorney General Elliot Richardson and Deputy Attorney General William Ruckelshaus refused the order and were promptly fired. Nixon finally appointed Solicitor General Robert Bork, who did the deed. The Washington Post noted that this “immediately raised prospects that the President himself might be impeached or forced to resign” [link].