With Washington still agog at the news that Michael Flynn was forced to resign his post as Donald Trump's national-security adviser, following revelations about his contacts with Russian officials, the Times, on Tuesday night, dropped another shocker on the capital. Citing four current and former American officials as their sources, the paper’s Michael S. Schmidt, Mark Mazzetti, and Matt Apuzo wrote, “Phone records and intercepted calls show that members of Donald J. Trump’s 2016 presidential campaign and other Trump associates had repeated contacts with senior Russian intelligence officials in the year before the election.”

U.S. intelligence agents, who discovered this information from electronic intercepts, haven’t so far turned up any evidence that the Trump campaign aides colluded with Russian efforts to influence the election, such as hacking, the Times report said. But it went on: “The intercepts alarmed American intelligence and law enforcement agencies, in part, because of the amount of contact that was occurring while Mr. Trump was speaking glowingly about the Russian president, Vladimir V. Putin.” One of the Trump associates picked up on the intercepts was Paul Manafort, Trump’s former campaign manager, the report said.

All this came at the end of a day that had been dominated by reactions to Flynn’s resignation, in which electronic intercepts also played a role. In a piece published Tuesday morning, my colleague Ryan Lizza wrote that a White House official he spoke to made Flynn out to be a “rogue operative, duping everyone in the White House about his contact with Russian officials.” This contact includes calls between Flynn and Sergey Kislyak, Russia’s Ambassador to Washington, on December 29th, the day that the Obama Administration imposed sanctions on some of Vladimir Putin’s cronies in response to revelations about Russian hacking during election season.

Flynn’s calls, which he and the White House originally claimed were no more than exchanges of pleasantries, turned out to have been recorded, presumably by the National Security Agency. We don’t know precisely what Flynn said to Kislyak, although reports say that the White House, the Justice Department, and the F.B.I.’s counterintelligence division have had access to transcripts. Last Thursday, the Washington Post reported that Flynn discussed the Obama Administration’s sanctions with Kislyak—a clear breach of diplomatic protocol and a possible breach of the law.

In retrospect, the revelation in the Post’s report made Flynn’s departure inevitable. But the more important point to grasp, as Lizza suggests, is that the “Flynn went rogue” narrative is risible. He was always a bit player in the much larger and more consequential story of Trump’s efforts to cozy up to Putin. His resignation, far from putting an end to that story, only makes more urgent the need for a proper investigation into the President’s ties to Russia. And the new revelations in the Times further underline the point.

As recently as last Friday, speaking to reporters on Air Force One, Trump claimed not to have seen the reports that Flynn brought up sanctions in his conversations with Kislyak. We now know, however, that F.B.I. agents interviewed Flynn in late January, and that the Justice Department then warned the White House that Flynn’s accounts of his phone calls were misleading and could potentially open him up to blackmail by the Russians. On Monday night, the Washington Post reported that Sally Yates, then the Acting Attorney General (whom Trump subsequently fired for refusing to defend his anti-Muslim travel ban), and “a senior career national security official” had delivered this warning to Donald McGahn, the White House counsel.

It’s far from clear what happened after Yates delivered this message. According to Sean Spicer, the White House spokesman, senior officials had been “reviewing and evaluating this issue on a daily basis, trying to ascertain the truth.” But what truth was there left to ascertain? If Trump regarded Flynn’s telephone diplomacy not as a rogue operation but as a faithful carrying out of his wish to curry favor with the Russians, there would be no reason to punish him. The only danger was that details of the Flynn-Kislyak conversations would leak, which would place Vice-President Mike Pence in an invidious position, as he had publicly claimed that the two men did not discuss sanctions. And, indeed, Trump strongly implied in a tweet on Tuesday morning that just such a leak was the real reason for Flynn’s departure. “ The real story here is why are there so many illegal leaks coming out of Washington?” he wrote. “Will these leaks be happening as I deal on N.Korea etc?”

One line of inquiry, then, is this one: Who knew what—and when—during the past couple of weeks? But, while the White House press corps gnaws at that bone, a much larger issue also needs to be addressed: What lies at the bottom of Trump's Putinophilia?

The benign explanation is that Trump and his aides think normalizing relations with Russia would serve America’s strategic interests and enable it to team up with the Kremlin in various parts of the world, such as in Syria. After Trump and Putin spoke in January, the Kremlin issued a statement saying, “The presidents spoke in favor of setting up genuine coordination between Russian and American actions with the aim of destroying Islamic State and other terrorist groups in Syria.” Although the policy of pursuing a rapprochement with Russia is unpopular in American foreign-policy circles, it does have some defenders. “Unlike China, Russia is not an emerging peer competitor to the United States,” Anatol Lieven, a British foreign-policy analyst, wrote in the Times on Tuesday. “A reduction of tension with Russia would allow the United States to concentrate on more important geopolitical issues.”

Another explanation for Trump’s behavior is that he sees the authoritarian Putin as a role model. Republican Senator Bob Corker, of Tennessee, who interviewed with Trump for the post of Secretary of State, offered a cautious endorsement of this idea in an interview with Politico on Monday. “I do think there is a degree of admiration for a strongman,” Corker said. “I’m sorry. And I think that part is somewhat real.” Corker also said that Trump is eager to demonstrate that he is a transformative figure, and that for “him to create a different kind of relationship with Russia, and especially someone who is strong like Putin, I think he views that as something that would show that he has the ability to do things that no other President has been able to do.”

A third theory is that the Russian government has some kind of hold over Trump. The unverified opposition-research dossier put together by a former British intelligence agent, which was published by BuzzFeed in January, said that the Kremlin may have gathered compromising material about the new President. On the Internet, there is now a cottage industry devoted to tracking and illustrating Trump’s alleged connections to Russian individuals and firms. Trump, of course, strenuously denies having any ties to Russia, and he has dismissed the dossier as “phony.”

This is an area heavy in speculation and light on confirmed facts, but we do know some things for sure. For one thing, American intelligence services believe that Russian intelligence agencies, at Putin’s direction, tried to help get Trump elected. It is also well established that Trump has had numerous financial dealings with rich and well-connected Russians. (For details on these dealings, see a long piece in The American Interest by the author and investigator James S. Henry.)