As Thursday’s extraordinary Senate Intelligence Committee appearance by Mr. Comey unfolded, it quickly became clear that the interpretation of Mr. Trump’s intentions at that moment and in other crucial interactions with Mr. Comey will be a central element of the investigations by both Congress and the special counsel, Robert S. Mueller III.

The ultimate outcome may boil down to a simple judgment: Was Mr. Trump criminal or clueless?

The president’s action and comments during the Oval Office session on Feb. 14 were a focal point of Mr. Comey’s public and written testimony. He noted that the president had said he “hoped” that Mr. Comey could see fit to end the Flynn inquiry. But Mr. Comey said he understood those words to mean much more.

“I took it as a direction,” said Mr. Comey, who later asked, “Why did he kick everyone out of the Oval Office?”

Senator Susan Collins, the Maine Republican who sits on the Intelligence Committee, has one theory potentially explaining why Mr. Trump excused the others. She noted that Mr. Comey had made sure that he met privately with Mr. Trump, then the president-elect, during a Jan. 6 meeting at Trump Tower to discuss an embarrassing, unsubstantiated intelligence dossier put together on Mr. Trump, excluding other national security officials who accompanied him.

“I think it is possible that it may have been F.B.I. director Comey who gave the impression to President Trump that their conversations should always be one on one because in their very first meeting it was Comey who cleared the room to have a discussion,” she said in an interview.