The measures embraced by Drs. Mecher and Hatchett would “result in significant disruption of the social functioning of communities and result in possibly serious economic problems,” Dr. Henderson wrote in his own academic paper responding to their ideas.

The answer, he insisted, was to tough it out: Let the pandemic spread, treat people who get sick and work quickly to develop a vaccine to prevent it from coming back.

Caught in the middle, C.D.C. leaders decided to conduct more research and survey community leaders around the country.

The administration ultimately sided with the proponents of social distancing and shutdowns — though their victory was little noticed outside of public health circles. Their policy would become the basis for government planning and would be used extensively in simulations used to prepare for pandemics, and in a limited way in 2009 during an outbreak of the influenza called H1N1.

Then the coronavirus came, and the plan was put to work across the country for the first time.

Dr. Mecher was a key voice on the “Red Dawn” email chain of public health experts in raising early warnings this year about the coronavirus outbreak and Mr. Trump’s reluctance to embrace shutdowns and social distancing. The shutdown this year is much bigger than Dr. Mecher and others imagined would be necessary or practical. Testing has been limited and some states issued social distancing orders even before confirming the coronavirus was spreading within their borders.

Dr. Markel called it “very gratifying to see our work used to help save lives.” But, he added, “it is also horrifying.”

“We always knew this would be applied in worst-case scenarios,” he said. “Even when you are working on dystopian concepts, you always hope it will never be used.”