In late 2016, then-FBI Director James Comey was ready to shut down a counterintelligence investigation the bureau had open on Michael Flynn, the retired general who was set to serve as President Donald Trump’s national security adviser.

Investigators “had not really substantiated anything particularly significant” in its investigation into Flynn’s possible links to foreign governments, Comey’s deputy, Andrew McCabe, told Congress late last year.

But the case took on new life just days into Flynn’s White House tenure.

As is now widely known, Flynn lied to two FBI agents during a Jan. 24, 2017 interview about his contacts several weeks earlier with Sergey Kislyak, the Russian ambassador at the time. Flynn, who resigned on Feb. 13, 2017, has since pleaded guilty in the special counsel’s Russia investigation to making false statements to the FBI. (RELATED: Here Is House Intel’s Long-Awaited Russia Report)

But newly unredacted portions of a report from the House Intelligence Committee show that FBI leaders faced a “conundrum” about how to proceed with the Flynn investigation.

The report cites testimony provided by both Comey and McCabe regarding Flynn.

Comey testified in March 2017 “that he authorized the closure of the [counterintelligence] investigation into General Flynn by late December 2016,” according to the report.

“However, the investigation was kept open due to the public discrepancy surrounding General Flynn’s communications with Ambassador Kislyak.”

McCabe testified that he was not aware that the closure of the Flynn investigation was “imminent” as of late 2016. But he told House Intel in a Dec. 19, 2017 interview that the FBI “really had not substantiated anything particularly significant against General Flynn.”

Flynn and three other Trump campaign associates — George Papadopoulos, Carter Page, and Paul Manafort — were subjects in the FBI’s counterintelligence probe at the time.

Why Flynn was being investigated is still not clear. A former director of the Defense Intelligence Agency, Flynn had accepted a paid appearance at a gala hosted in Moscow in Dec. 2015 by RT, the Kremlin-controlled news agency. Flynn sat next to Russian president Vladimir Putin at the event.

Flynn spoke to Kislyak by phone on several occasions in late Dec. 2016 about a round of sanctions that the Obama administration had placed against Russia for meddling in the election.

Flynn initially denied to others in the administration that the conversations involved U.S. sanctions against Russia. But intercepts of Kislyak’s phone calls showed otherwise. The story blew up on Jan. 12, 2017, when Washington Post columnist David Ignatius reported that Flynn and Kislyak indeed discussed sanctions. Ignatius’s leaker was a U.S. government official who has yet to be identified.

Comey directed McCabe to set up an interview with Flynn at the White House in an effort to explain the discrepancy in Flynn’s statements about his Kislyak conversations.

The interview took place on Jan. 24, 2017. One of the agents who interviewed Flynn was Peter Strzok, the former FBI counterintelligence division official who is currently ensnared in scandal for sending anti-Trump text messages to an FBI lawyer.

Both Comey and McCabe told the House Intel panel that the agents did not detect deception from Flynn during the White House interview.

Comey said that they interviewers “discerned no physical indications of deception. They didn’t see any change in posture, in tone, in inflection, in eye contact. They saw nothing that indicated to them that he knew he was lying to them.”

McCabe confirmed the FBI agents’ perception of the Flynn interview.

“The two people who interviewed [Flynn] didn’t think he was lying.”

He noted that the lack of apparent deception “was not [a] great beginning of a false statement case,” according to the House Intel report.

McCabe also described the “conundrum that we faced on their return from the interview is that although [the agents] didn’t detect deception in the statements that he made in the interview … the statements were inconsistent with our understanding of the conversation that he had actually had with the ambassador.'”

The implications of Comey and McCabe’s initial assessment of the Flynn investigation are unclear. Supporters of the retired general are likely to argue that the White House interview was a last-ditch effort to trap Flynn into committing a crime. Flynn’s critics have maintained that his decision to lie about his Kislyak contacts is evidence of a larger cover-up.

An attorney for Flynn declined to discuss the House Intel report because of the special counsel’s ongoing investigation. Flynn is cooperating with the investigation as part of his plea deal.

Follow Chuck on Twitter

Content created by The Daily Caller News Foundation is available without charge to any eligible news publisher that can provide a large audience. For licensing opportunities of our original content, please contact licensing@dailycallernewsfoundation.org.