Olympic officials will announce their decision on Dec. 5. If they do not bar Russia completely from the coming Winter Olympics in Pyeongchang, South Korea, they are likely to keep all Russian emblems out of the Games: The Russian flag would not fly at the opening and closing ceremony, Russian athletes would compete in neutral uniforms and the Russian anthem would not be played. Such restrictions, Russian officials have said, would be tantamount to an outright ban, and Russia would consider boycotting the 2018 Olympics.
For the following week, as the Sochi Games approached, alongside admirations of his new Samsung smartphone and criticisms of Olympic cafeteria food, Dr. Rodchenkov recorded his frustration that officials had not clearly outlined their plans to transport from Moscow the hundreds of ounces of clean urine that top athletes had for months collected in baby food jars and old soda bottles — urine that was the linchpin to what he repeatedly referred to as "the Sochi plan.”
On Feb. 1, he followed instructions that Mr. Nagornykh, the deputy minister, had given him at the Azimut hotel the night before. Dr. Rodchenkov inspected the building adjacent to his lab, controlled by the Federal Security Service, he said. The stockpiled urine had arrived in Sochi and was surreptitiously stored there, he wrote, but he was maddened that the samples were not sorted by sport or alphabetized by each corresponding athlete’s name.
"Nothing is ready there,” he wrote. "I completed a full inventory.”
On Feb. 3, four days before the Sochi Games began, Dr. Rodchenkov’s preparations culminated with his presentation to Mr. Mutko, the sports minister. In a meeting at Mr. Mutko’s office at the local organizing committee’s headquarters, Dr. Rodchenkov wrote that day, he had handed Mr. Mutko a copy of the "Duchess list,” naming the dozens of Russian Olympians who were ingesting the drug cocktail and would have their incriminating urine swapped out with their prestocked clean urine.
Following multiple investigative reports published last year, Russia’s coordinated cheating has been accepted as fact among top Olympic officials, in spite of a largely defiant response from Russian authorities that has grown fiercer in recent weeks. This fall, Russia criminally charged Rodchenkov with abuse of authority and indicated it would request his extradition. Authorities had previously seized his property in Moscow, where his family remains.
Russian officials have suggested Dr. Rodchenkov acted alone in tampering with more than 100 incriminating urine samples in Sochi, an act which has so far led the global officials to order Russia to return 11 Olympic medals. "One can hardly steal a victory that has already been won,” a Kremlin spokesman said Monday about those disqualifications.
But during the Games, Dr. Rodchenkov documented multiple meals with Mutko and acted with familiarity, according to his daily notes. "I ate Mutko’s grapes,” he wrote on Feb. 17 about a lunch at which he had already eaten sea bass fillet and mutton soup. "Everyone is exhausted.”
Dr. Rodchenkov and his lawyer say the contemporaneous notes make clear he was a foot soldier in a system that was controlled at the highest levels of the state. Documents published Monday by the International Olympic Committee indicate they, too, accept his account.
"Dr. Rodchenkov was telling the truth when he provided explanations of the cover-up scheme he managed,” Olympic officials wrote in the first disciplinary decision related to the Russian doping scandal, justifying a lifetime ban for the 19th Russian athlete so far disciplined for the Sochi schemes.
Dr. Rodchenkov is living in an undisclosed location in the United States under protection by American authorities. His lawyer said Dr. Rodchenkov had been fully cooperative with American and international agencies concerning Russia’s doping program.
"If the I.O.C. fails to act to severely punish this frontal assault on the integrity of the Olympics, it will forever lose the moral authority to punish any cheaters,” said the lawyer, Jim Walden, of the firm Walden, Macht and Haran.
Dr. Rodchenkov told The Times last year that he had recorded the details of his work in Moscow somewhat mindfully, and not on a computer — as his friend Nikita Kamayev, Russia’s former antidoping chief who died suddenly in 2016, had done. It was Mr. Kamayev who gave Dr. Rodchenkov the black and gold Waterman pen he used for his diaries.
Dr. Rodchenkov attributed Mr. Kamayev’s sudden death to his announcement that he was writing a book, from which Dr. Rodchenkov said he tried to dissuade him.
"I told him, I’m not writing with a computer,” Dr. Rodchenkov said in May 2016. "I’m writing with your pen.”