LATE fall was a frantic period for New York Times reporters covering the country’s secretive national security apparatus. Working sources at the F.B.I., the C.I.A., Capitol Hill and various intelligence agencies, the team chased several bizarre but provocative leads that, if true, could upend the presidential race. The most serious question raised by the material was this: Did a covert connection exist between Donald Trump and Russian officials trying to influence an American election?

One vein of reporting centered on a possible channel of communication between a Trump organization computer server and a Russian bank with ties to Vladimir Putin. Another source was offering The Times salacious material describing an odd cross-continental dance between Trump and Moscow. The most damning claim was that Trump was aware of Russia’s efforts to hack Democratic computers, an allegation with implications of treason. Reporters Eric Lichtblau and Steven Lee Myers led the effort, aided by others.

Conversations over what to publish were prolonged and lively, involving Washington and New York, and often including the executive editor, Dean Baquet. If the allegations were true, it was a huge story. If false, they could damage The Times’s reputation. With doubts about the material and with the F.B.I. discouraging publication, editors decided to hold their fire.

But was that the right decision? Was there a way to write about some of these allegations using sound journalistic principles but still surfacing the investigation and important leads? Eventually, The Times did just that, but only after other news outlets had gone first.

I have spoken privately with several journalists involved in the reporting last fall, and I believe a strong case can be made that The Times was too timid in its decisions not to publish the material it had.

I appreciate the majority view that there wasn’t enough proof of a link between Trump and the Kremlin to write a hard-hitting story. But The Times knew several critical facts: the F.B.I. had a sophisticated investigation underway on Trump’s organization, possibly including FISA warrants. (Some news outlets now report that the F.B.I. did indeed have such warrants, an indication of probable cause.) Investigators had identified a mysterious communication channel, partly through a lead from anti-Trump operatives

At one point, the F.B.I. was so serious about its investigation into the server that it asked The Times to delay publication. Meanwhile, reporters had met with a former British intelligence officer who was building the dossier. While his findings were difficult to confirm, Times reporting bore out that he was respected in his craft. And of his material that was checkable, no significant red flags emerged. What’s more, said one journalist frustrated with the process, a covert link seemed like a plausible explanation for the strange bromance between Trump and Putin.

There were disagreements about whether to hold back. There was even an actual draft of a story. But it never saw daylight. The deciding vote was Baquet’s, who was adamant, then and now, that they made the right call.

“We heard about the back-channel communications between the Russians and Trump,” he said. “We reported it, and found no evidence that it was true. We wrote everything we knew — and we wrote a lot. Anybody that thinks we sat on stuff is outrageous. It’s just false.”

I don’t believe anyone suppressed information for ignoble reasons, and indeed The Times produced strong work on former campaign chairman Paul Manafort. But the idea that you only publish once every piece of information is in and fully vetted is a false construct.

If you know the F.B.I. is investigating, say, a presidential candidate, using significant resources and with explosive consequences, that should be enough to write. Not a “gotcha” story that asserts unsubstantiated facts. But a piece that describes the nature of the investigations, the unexplained but damning leads, with emphasis on what is known and what isn’t.

Running every detail of the dossier, as BuzzFeed did, would have been irresponsible. Writing about a significant investigation would not. Weeks after The Times had the goods, Franklin Foer of Slate and David Corn of Mother Jones each took a turn at such pre-election articles. Their stories may not have been precisely what The Times would have done, but they offered a model.

If The Times didn’t write about ongoing investigations, it wouldn’t have produced the excellent scoop on Trump associates and Russia that broke Thursday night. Nor would it have so relentlessly documented the F.B.I.’s pursuit of Hillary Clinton’s emails until all facts were resolved. That investigation was fair game, and so was Trump’s.

A wave of readers over the past week have challenged The Times’s decision to sit on its reporting about the dossier. Among them was Michael Russo of Brooklyn, who had this to say:

I can appreciate that journalistic diligence requires your paper to describe these memos as “unsubstantiated.” But the “unsubstantiated” allegations described in this article have been circulating for months. While your editors made a value judgment about the veracity of these claims, American intelligence agencies apparently took the memos seriously enough to open their own investigations. How is this not newsworthy in its own right?

There is an unsettling theme that runs through The Times’s publishing decisions. In each instance, it was the actions of government officials that triggered newsroom decisions — not additional reporting or insight that journalists gained. On the server, once the F.B.I. signaled it had grown wary of its importance — without giving conclusive evidence as to why — the paper backed off. Weeks later, the Senate Democratic leader, Harry Reid, publicly admonished the F.B.I. for being secretive about its probe of Trump. That gave The Times cover to write what it knew about the bureau’s investigation into the bank server.

It was the same pattern on the dossier. Only after learning from CNN that Trump and President Obama had been briefed on the document did The Times publish what it had known for months. Its confidence in the material had not changed, nor did its editors know whether the top level briefing meant the government believed the information was true. But the briefing became justifiable cause to publish.

In this cat-and-mouse game between government and press, the government won.

After-action insights are easier than in-the-moment decisions. Back then, the media still thought Trump was a weak challenger to Clinton, a mind-set that might have made taking the risk of publishing explosive allegations all the more fraught.

But it’s hard not to wonder what impact such information might have had on voters still evaluating the candidates, an issue I chided The Times for not pursuing enough in an earlier column. Would more sources have come forward? Would we already know the essential facts?

If the new president was in fact colluding with a foreign adversary, journalists and investigators should feel enormous pressure to conclusively establish that fact. If it is not true, both Trump and the country deserve to have this issue put to rest.

Updated at 5:55 p.m. to include clarifying information on the Times investigation.