It was shortly after federal agents confronted him in May outside a boutique hotel in Lubbock, Texas, seizing his cellphone with a warrant, that Stewart Rhodes, the leader of the Oath Keepers militia, made a bold decision: Even though he had just gotten undeniable proof that he was under investigation, he agreed to be questioned about his — and his militia’s — role in the Jan. 6 attack on the Capitol.

Against the advice of a lawyer, Mr. Rhodes spoke freely with the agents about the Capitol assault for nearly three hours, he said in an interview on Friday. Mr. Rhodes said that he denied that he or any other Oath Keepers had intended to disrupt Congress’s certification of the Electoral College vote — the chief accusation the government has lodged against 16 members of the group who are charged with conspiracy.

He also said he told the agents that members of his militia went into the building only after they had heard that someone had been shot inside and wanted to render aid. (A New York Times visual investigation of the events of Jan. 6 did not find evidence of Mr. Rhodes’s claims.)

“I did express frustration that some of my guys went in,” Mr. Rhodes said, noting that he told the F.B.I. that those who breached the Capitol had “gone off mission.” But then he quickly added, “There were zero instructions from me or leadership to do so.”

For months, the government has quietly acknowledged that investigators have been scrutinizing the role that Mr. Rhodes played in the Jan. 6 assault, but the fact that he voluntarily submitted to an F.B.I. interview was a new step in the inquiry. In court papers connected to the case of his associates, Mr. Rhodes has been identified as Person 1 and prosecutors have described how he was in direct communication with some suspects before, during and after the assault.

They have also said that he sent members of the group encrypted messages assuring them that “well-equipped Q.R.F.s” — or quick-reaction forces — would be standing by outside of Washington on Jan. 6 “in case of worst case scenarios.”

Speaking with investigators in the middle of a criminal inquiry is a risk even though Mr. Rhodes had a lawyer, Kellye SoRelle, present with him. Mr. Rhodes said that he was not the only Oath Keeper leader to have talked with federal agents in recent weeks. After he was questioned, one of his top lieutenants, a man he identified as Whip (and who is known as Person 10 in court papers), also spoke voluntarily with the F.B.I.

“We’ve got nothing to hide,” Mr. Rhodes explained. “We did nothing wrong.”

A spokeswoman for the Justice Department declined to comment on the interviews.

The revelation that two Oath Keeper leaders — who have not been charged — have been questioned by the F.B.I. comes at a kind of inflection point for the Oath Keepers’ case, one of the most prominent prosecutions stemming from the Capitol assault.

Earlier this month, most of the defendants challenged the viability of the government’s charges and one asked the presiding judge, Amit P. Mehta, to move his trial out of Washington, arguing that too many local residents suffered from “Trump Derangement Syndrome.” Judge Mehta issued an order on Tuesday saying that the 16 defendants would be tried in two groups, one tentatively set to begin in January, the other three months later.

At the same time, however, at least three Oath Keepers have pleaded guilty in the case and have agreed to cooperate with the government’s sprawling investigation of the group. At a recent hearing, prosecutors told Judge Mehta that they were in plea negotiations with several other members and could not rule out further charges.

Despite the flurry of activity, prosecutors overseeing the investigation of Mr. Rhodes have long admitted that they have struggled to make a case against him. His activities seemed to stay within the boundaries of the First Amendment, one official with knowledge of the matter said.

Known for his black eye patch — the result of a gun accident — Mr. Rhodes, who attended Yale Law School after serving in the military, founded the Oath Keepers in 2009, after the election of former President Barack Obama. For years, he has earned a reputation as a leader in the right-wing “patriot” movement, often spewing incendiary rhetoric.

But after Donald J. Trump was elected, he and his members seemed to pivot from their anti-government views and embrace the new spirit of nationalism and suspicions of a deep-state conspiracy that had taken root in Mr. Trump’s administration.

Mr. Rhodes was particularly vocal in supporting the former president’s repeated lies that the 2020 elections were marred by fraud and that President Joseph R. Biden Jr.’s victory was illegitimate.

One week after Election Day, for instance, Mr. Rhodes told the conspiracy theorist Alex Jones that he had men stationed outside Washington prepared to act at Mr. Trump’s command. And at a rally in the city on Dec. 12, he called on Mr. Trump to invoke the Insurrection Act.

Then, two days before the Capitol attack, Mr. Rhodes issued a “call for action” on the Oath Keepers’ website, urging “all patriots who can be in D.C.” to “stand tall in support of President Trump’s fight to defeat the enemies foreign and domestic who are attempting a coup.”

In the same communiqué, he announced that the Oath Keepers would be sending “security teams” to provide protection to “V.I.P.s” at events surrounding the political rallies in Washington on the day before and the day of the riot. Members of the group, including some who have been charged, did work as guards for Mr. Trump’s close ally and adviser Roger J. Stone Jr.

Mr. Rhodes has long predicted his own arrest, noting at a speech at the Texas-Mexico border in March that he might face charges in connection with the Jan. 6 attack.

“I may go to jail soon,” he told the crowd. “Not for anything I actually did, but for made-up crimes.”