Late September 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.