As the Allied troops advanced through France in November 1944, three experts in biological weapons huddled, by candlelight, in a grand apartment in Strasbourg, France, guarded by US soldiers.

The scientists were poring through documents left behind by Dr. Eugen Haagen, a high-ranking Nazi who specialized in weaponizing deadly viruses. They were looking for evidence of the Third Reich’s progress in atomic and biochemical warfare; what they found were chronicles of devastating carnage.

“Of the 100 prisoners you sent me, 18 died in transport,” Haagen wrote in a memo dated Nov. 15, 1943. “Only 12 are in a condition suitable for my experiments. I therefore request that you send me another 100 prisoners, between 20 and 40 years of age, who are healthy and in a physical condition comparable to soldiers. Heil Hitler.”

Haagen was once a world-renowned genius who had won a fellowship from the Rockefeller Foundation in New York City, who had been shortlisted for a Nobel Prize, who helped create the first vaccine for yellow fever. Yet here was evidence that he — and could it only have been just one doctor? — had been conducting medical experiments on live humans.

Samuel Goudsmit, leader of this investigative unit, made a list. Haagen was at the top, and he added any names referenced or copied on Haagen’s memos, including Dr. Kurt Blome, the Third Reich’s deputy surgeon general, and Walter Schreiber, the surgeon general. These men were now among America’s most wanted — but not in the way one might assume.

Within the year, hundreds of the Third Reich’s upper echelon would be relocated to the United States, where they would be given excellent jobs, healthy salaries, and all the benefits of living in a free society.

It was a secret program known as Paperclip, and it remains one of the most complicated and controversial epochs in American history. And, still, one of the most classified.

In her new book “Operation Paperclip: The Secret Intelligence Program to Bring Nazi Scientists to America” (Little, Brown and Company), author Annie Jacobsen uses newly released documents, court transcripts, and family-held archives to give the fullest accounting yet of this endeavor — one shared by the British, the French, and the Russians, all of whom enlisted and embraced top Nazis.

Wernher von Braun, the Nazi scientist crucial to the development of the V-2 rocket — which held a payload of 2,000 pounds and flew five times beyond the speed of sound — saw it coming: In March 1945, he conscripted two friends to stash his most important research out in an abandoned mine; when Germany lost, von Braun said, he’d use these documents to broker a new life in the United States.

He knew that no matter what atrocities were eventually discovered, no major world power would refuse the technological advances made by the Nazis — nor could they afford not to know how to combat them, vaccinate against them, outpace them.

That same year, the Department of Defense created a top-secret, elite task force called the Joint Intelligence Objectives Agency, or JOIA. They were subordinate to the Joint Intelligence Committee, which briefed the Joint Chiefs of Staff on national security threats.

“To understand the mind-set of the Joint Intelligence Committee,” Jacobsen writes, “consider this: Within one year of the atomic bombing of Hiroshima and Nagasaki, the JIC warned the Joint Chiefs of Staff that the United States needed to prepare for ‘total war’ with the Soviets — to include atomic, chemical, and biological warfare — and they even set an estimated start date of 1952.”

As of May 1945, Werner von Braun was No. 1 on America’s list for desired Nazi rocket scientists. When he surrendered to US forces on May 2 — having voluntarily decamped from a luxury ski resort in the Alps — von Braun and his colleagues were treated to a hearty breakfast of eggs, coffee and bread, then given freshly made beds in which to sleep.

“I did not expect to be kicked in the teeth,” von Braun later told an American reporter. “The V-2 was something we had and you didn’t have. Naturally, you wanted to know all about it.”

Also at the top of the list was Dr. Kurt Blome, Hitler’s head of cancer research and a diehard Nazi. He was discovered at a checkpoint on May 17, 1945, and in his initial interrogation, Blome admitted that he had seen experiments “which led to later atrocities e.g. mass sterilization, gassing of Jews.”

Then came the capture of Georg Rickhey, an expert on the Third Reich’s impenetrable underground bunkers. Rickhey was interrogated by Col. Peter Beasley, who told him, “As an American officer, I want my country to have full possession of all your knowledge. To my superiors, I shall recommend that you be taken to the United States.”

Among those tasked with finding and apprehending the most wanted men in the Third Reich — and the number of government agencies that became involved — there was deep discord about the morality of Operation Paperclip.

Jacobsen accessed the transcript of a volatile meeting, secretly recorded, at the War Department. The names were redacted.

“One of the ground rules for bringing them over,” said one general, “is that it will be temporary, and at the return of their exploitation they will be sent back to Germany.”

“I’m opposed,” said another general. “And Pop Powers [nickname of an unknown official] is opposed, the whole War Department is opposed.”

It didn’t matter. Unofficial US policy held that it was imperative to secretly procure those Nazis who could accelerate America’s scientific, technological and economic advancement.

This was an increasingly delicate operation. On May 7, 1945, Life magazine had run a series of photos from the concentration camps, and the official US line held that countries such as Uruguay and Argentina, which were welcoming Nazi refugees, should turn them over to stand trial.

Simultaneously, the US government was learning more and more about just what the Nazis had done: the extermination of millions of Jews; the mass sterilization, the live experiments and operations conducted without anesthesia on humans code-named “adult pigs,” the systematic yanking of gold teeth, the slave labor and starvation, the drowning of men in ice-cold tubs and the many failed attempts to resurrect them, the exploding bodies forced into high-altitude chambers in efforts to master space flight.

“German science presents a grim spectacle,” wrote Dr. Leopold Alexander, a Viennese Jew who immigrated to the US in 1933. When the US entered the war, Alexander enlisted, and at its end was sent to Germany to determine what the Nazis had wrought and learned medically.

“Grim for many reasons,” he continued. “First it became incompetent and then it was drawn into the maelstrom of depravity of which this country reeks — the smell of concentration camps, the smell of violent death, torture and suffering.”

He went on to call the Third Reich’s experimentation “really depraved pseudoscientific criminality . . . It sometimes seems as if the Nazis had taken special pains in making practically every nightmare come true.”

Meanwhile, the Allies held elite Nazis in two luxurious locales: the Palace Hotel in Luxembourg, renamed “Ashcan,” and Crane Mountain Castle in Hesse, Germany, renamed “Dustbin.”

Here, the most warped and wicked Nazis lounged in well-appointed rooms, strolled through apple orchards, played chess, smoked and drank, and gave each other lectures in grand halls. In the mornings, Hitler’s doctor taught a workout class.

In June 1945, officers at Dustbin put out an alert for Dr. Otto Ambros, valuable for his work with toxic gases — specifically tabun, developed by the Nazis and a chemical far more lethal than sarin. Ambros was picked up by an American soldier, who then drove him to a meeting in Heidelberg with members of the US Chemical Warfare Service.

So comfortable were these negotiations that when the US contingent told Ambros to retrieve the documents relating to tabun production, they let him drive off on his own. Ambros never returned; instead, he fled to an area controlled by the French, who let him return to civilian life in Germany.

The War Department moved quickly. In July, they made their top-secret project official, circulating a memo titled “Exploitation of German Specialists in Science and Technology in the United States.”

Jacobsen writes that President Truman “was not made aware of the initiative,” which was initially known as Operation Overcast.

Months later, when the War Department began tagging the files of their most reprehensible Nazi recruits with paper clips as intra-office code — these Nazis were truly to be smuggled in, made known to no other bureaucracies — the program became known as Operation Paperclip.

Meanwhile, Truman ordered the Department of Commerce to propagandize the advances made by the Nazis, ones that were now making Americans’ lives easier, more comfortable: Women could buy stockings that wouldn’t run, butter churned so fast and juice now sterilized so simply that there would be an abundance for all. Electrical equipment that had once been the size of crates was no bigger than your smallest finger.

By January 1946, two months after the Nuremberg trials had begun, there were more than 160 Nazis — many with their families — living and working in the United States.

A good number were housed at a facility called Hilltop in Dayton, Ohio, where many complained they were little more than “caged animals.” The US military scientists working alongside them were disgusted by their new colleagues, expressing “emotions . . . ranging from vehemence to frustration.”

The other group — at 115, the largest — was a team of rocket scientists held on Fort Bliss in Texas. Their leader was Wernher von Braun, who, it turned out, really loved America. He was enthralled with the desert and the open-air jeeps driven by Army personnel. He became an evangelical Christian. He was permitted to return to Germany to marry his 18-year-old cousin — von Braun was 46 — and bring her back to the US. If he had one complaint, it was his research budget.

As he later said, while working for the Third Reich “we’d been coddled. Here they were counting pennies.”

In November 1946, shortly after 10 Nazis were executed at Nuremberg by US Master Sgt. John C. Woods (“I hanged those 10 Nazis . . . and I am proud of it”), news broke that the US had smuggled hundreds of Nazis into the country, and that about 1,000 more were coming. (The final count was close to 1,600.) The government attempted damage control, then message control: These men, so mild-mannered with their silver hair and American sport jackets, had never been members of the Nazi party. The Army disseminated pictures of the men and their families engaged in wholesome outdoor activities, and any reporter requesting an interview had to submit their copy, pre-publication, to the army for approval.

Not everyone was fooled. Eleanor Roosevelt publicly decried the program, as did Albert Einstein. By March 1947, Paperclip had generated such lacerating public opinion that General Eisenhower, then the US Army chief of staff, demanded a briefing. It lasted 20 minutes, and upon emerging, Eisenhower said he approved of the project.

The legacy of Paperclip, Jacobsen writes, speaks to the triumph of pragmatism and self-interest above unthinkable atrocity.

Wernher von Braun helped get us to the moon; in the years before the landing, he was photographed with President Kennedy. Heinrich Rose and Konrad Buttner, two hardcore Nazis, conducted experiments for the US on how best to protect soldiers in atomic warfare.

Today, the Space Medicine Association and the National Space Club continue to bestow awards named after Nazis. When Jacobsen asked Steve Griffin, head of the National Space Club, why they memorialize Nazi Kurt Debus in this way, he was dispassionate and logical.

“Simple as it is,” he said, “Kurt Debus is an honored American.”