Meanwhile, Hopkins’ personal life suffered terribly. In October 1937, his second wife, Barbara, died of cancer, and in December surgeons removed two-thirds of Hopkins’ stomach in order to stave off the same disease. The gangly Iowan survived, but his health remained fragile for the rest of his life. Encouraged by Roosevelt, who originally hoped to retire at the end of his second term, Hopkins briefly entertained thoughts of the presidency. His hopes were further legitimized when Roosevelt appointed him secretary of commerce in December 1938. Hopkins’ tenure as commerce secretary, however, proved frustrating and brief. Afflicted with hemochromatosis–a result of his chronically inadequate digestive system–he was unable to fully dedicate himself to his job and by the following August was at death’s door. Roosevelt arranged for the best navy doctors to treat his friend. Hopkins rallied, but his ordeal drained him of political ambition. He resigned his cabinet position in August 1940, determined to serve Roosevelt and his country in other ways for as long as possible.

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Hopkins’ assignment to meet with Churchill bypassed normal diplomatic channels. He held no official position, and when reporters asked the president if Hopkins was to be the next ambassador to Great Britain, Roosevelt answered, "You know Harry isn’t strong enough for that job." Recent events, however, had left a serious void in communication between the two nations. Ambassador Joseph P. Kennedy, Sr., had resigned, and the British ambassador to the United States, Lord Lothian, had died just days after Roosevelt received Churchill’s pivotal letter. Unable to meet with his British counterpart himself, Roosevelt told the press he was sending Hopkins to London "so that he can talk to Churchill like an Iowa farmer."

The mission was indicative of the special trust that Roosevelt put in Hopkins. Unassuming and plainspoken, Hopkins enjoyed a unique relationship with the chief executive. Roosevelt had other advisers, but he found Hopkins perfect company and liked to discuss important matters with him informally. Hopkins was unswervingly loyal to the president, who in turn often heeded his friend’s advice on significant policy issues. The president’s decisions, however, were clearly his own. For example, Roosevelt appointed General Dwight D. Eisenhower chief of Operation Overlord (the 1944 Normandy invasion plan) instead of General George C. Marshall, despite the opposition of Hopkins and many others, including Churchill. Meanwhile, the public regarded Hopkins as something of a "mystery man," as Time magazine described him in 1944, consumed by a strange illness and privy to the war’s many secrets.

Noticeably ill during a visit with the president in May 1940, Hopkins spent the night in a White House suite. At one time President Abraham Lincoln’s study, the suite was just down the hall from Roosevelt’s room. Hopkins lived there for the next three and a half years. When he married for the third time in July 1942, his wife, Louise, joined him and his daughter Diana in the White House. The family remained there until December 1943, when Harry rented a house in nearby Georgetown. Other members of Roosevelt’s circle, such as Rexford Tugwell and Henry Morgenthau, came to accept Hopkins’ closeness to the president as a fact of Washington life. Not everyone, however, was happy with the arrangement. Harold Ickes resented Hopkins’ insider role, and the two remained at odds for years. "I do not like him," Ickes once noted in his diary, "and I do not like the influence that he has with the president." Wendell Willkie, Roosevelt’s opponent in the 1940 presidential campaign, asked Roosevelt why he placed such faith in Hopkins when he knew that others resented it. The president told Willkie that if he ever became president, "You’ll learn what a lonely job this is, and you’ll discover the need for someone like Harry Hopkins who asks for nothing except to serve you."

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