Justice Samuel Alito has multiple times over the course of questioning sounded sympathetic toward Trump's positions.

He also seemed to raise concerns about former presidents suffering the burden of having to go through a trial if they are criminally charged.

"That may involve great expense, and it may take up a lot of time, and during the trial the former president may be unable to engage in other activities that the former president would want to engage in, and then the outcome is dependent on the jury, the instructions to the jury and how the jury returns a verdict, and then it has to be taken up on appeal," Alito said at one point.

In his final question to government attorney Michael Dreeben, Alito seemed to suggest that Trump's prosecution could serve to incentivize future presidents to try and unlawfully remain in office in order to avoid prosecution by their successors.

"Now, if an incumbent who loses a close, hotly contested election knows that a real possibility after leaving office is not that the president is going to be able to go off into a peaceful retirement -- but that the president may be criminally prosecuted by a bitter political opponent. Will that not lead us into a cycle that destabilizes the functioning of our country as a democracy?" Alito asked.

"I think it is exactly the opposite, Justice Alito," Dreeben replied, noting Trump and his allies filed dozens of lawful challenges to the results of the election and lost.

"There is an appropriate way to challenge things through the courts with evidence," Dreeben said. "If you lose, you accept the results, that has been the nation's experience, I think the court is well familiar with that."

Asked by Justice Elena Kagan what "core" executive functions have "absolute protection," government attorney Michael Dreeben said they include pardon power, veto, foreign recognition and appointments.

"Congress cannot say you can't appoint a federal judge who hasn't received a certain diploma, hasn't achieved a certain age," he said.

Commander in chief is also on the list, he said, though added that Congress has "substantial authority in the national security realm."

"I think that there may be some aspects like directing troops on the field in which the president's power is completely unreviewable," he said.

As the justices wrestle with immunity, they are posing another question to lawyers: Can presidents pardon themselves?

Justice Neil Gorsuch asked Trump attorney John Sauer about the possibility, saying presidents could be incentivized to do so if they fear their successors could prosecute them for actions they took while in office.

"I didn't think of that until your honor asked it," Sauer said. "That is certainly incentive that might be created."

Michael Dreeben, arguing for the government, was later asked for his view on whether the president has such authority.

"I don't believe the Department of Justice has taken a position," Dreeben said. "The only authority that I'm aware of is a member of the Office of Legal Counsel wrote on a memorandum that there is no self-pardon authority. As far as I know, the department has not addressed it further, and the court had not addressed it either."

Justice Samuel Alito addressed the "layers of protection" against bad faith prosecutions raised by the DOJ.

"I'm going to start with what the D.C. Circuit said. So, the first layer of protection is that attorneys general and other justice department attorneys can be trusted to act in a professional and ethical manner, right?" Alito said. "How robust is that protection?"

Alito continued that the "vast majority" of attorneys general and justice department attorneys "take their professional ethical responsibilities seriously" but that there have been exceptions.

In response, DOJ attorney Michael Dreeben agreed that there have been "rare exceptions" and said that "we're talking about layers of protection."

"I do think this is the starting point, and if the court has concerns about the robustness of it, I would suggest looking at the charges in this case," he said.

"The allegations about the misuse of the Department of Justice to perpetuate election fraud show exactly how the Department of Justice functions in the way that it is supposed to," Dreeben said. "Petitioner is alleged to have tried to get the Department of Justice to send fraudulent letters to the states to get them to reverse electoral results."

Justice Clarence Thomas opened questioning by getting to the heart of the case: where is the "source" of presidential immunity and how would the court come to decide what acts fall under that scope.

First, he asked Trump's attorney to be "more precise as to the source" of supposed presidential immunity.

John Sauer responded that it comes from the executive vesting clause of the Constitution.

Thomas then pressed how exactly the court would "determine what an official act is," to which Sauer said acts fall within the “outer perimeter” of a president's official duties.