Most of the Supreme Court’s decision on Monday about executive immunity was focused like a laser on former President Donald J. Trump’s indictment on charges of plotting to subvert the 2020 election.
But a small part was also relevant to the other federal case that Mr. Trump is facing — the one in Florida in which he stands accused of illegally holding on to a highly sensitive trove of classified documents after he left office and then obstructing efforts to retrieve them.
In a brief concurrence to the immunity opinion, Justice Clarence Thomas said he was joining the majority’s position that Mr. Trump enjoyed a substantial amount of protection from criminal prosecution. But he advanced his own reason for making that decision: He suggested that the special counsel, Jack Smith, who is handling the two federal matters against Mr. Trump, was given his job without a legal basis.
That same question is currently being considered by Judge Aileen M. Cannon, who is presiding over the classified documents case in Federal District Court in Fort Pierce, Fla. Not much more than a week ago, Judge Cannon held two days of unusual hearings in Fort Pierce specifically to discuss the issue of whether Mr. Smith had been properly funded and appointed as special counsel.
Justice Thomas never explicitly mentioned Judge Cannon or the documents case in his nine-page concurrence. But he did recommend that “lower courts” look into the “essential questions concerning the special counsel’s appointment” — which is exactly what happened at the hearings in Fort Pierce.
The justice also declared that there should be consequences if Mr. Smith was indeed appointed without a legal basis.
“If there is no law establishing the office that the special counsel occupies, then he cannot proceed with this prosecution,” Justice Thomas wrote in what seemed to be a reference to the election interference case that could easily hold sway in the classified documents case as well.
“A private citizen cannot criminally prosecute anyone,” he wrote, “let alone a former president.”
Justice Thomas has faced criticism for hearing issues related to Mr. Trump given that his wife, Virginia Thomas, known as Ginni, helped shape the effort to overturn the 2020 election. While Mrs. Thomas has played no role in the classified documents case, evidence has emerged that she pushed hard to keep Mr. Trump in office during the chaotic weeks between the last election and the Jan. 6 attack on the Capitol.
By signaling that Mr. Smith’s appointment was in doubt, Justice Thomas adopted Mr. Trump’s own position on the issue. In their arguments in front of Judge Cannon last month, the former president’s lawyers claimed that Mr. Smith had not been named to his post by the president or confirmed by the Senate like other federal officers.
They also said that Attorney General Merrick B. Garland, who gave Mr. Smith his job, had no legal power to do so on his own.
Mr. Smith’s deputies have countered that under the appointments clause of the Constitution, agency heads like Mr. Garland are authorized to name “inferior officers” like special counsels to act as their subordinates.
Justice Thomas in his concurrence questioned whether Mr. Smith was in fact an “inferior officer” and even whether his appointment was valid “unless a statute created the special counsel’s office and gave the attorney general the power to fill it.”
Despite Justice Thomas’s concerns, courts reaching back to the early 1970s have repeatedly rejected efforts to question the legality of independent prosecutors. Those have included the Supreme Court upholding the appointment of Leon Jaworski, one of the special prosecutors who investigated the Watergate scandal, in a decision that was largely focused on the issue of President Richard Nixon’s claims of executive privilege.
Judges have also tossed out efforts to invalidate the work of special counsels like Robert S. Mueller III, who examined connections between Russia and Mr. Trump’s 2016 campaign, and David C. Weiss, who has brought two criminal cases against Hunter Biden, President Biden’s son.