In a way, JFK's first two years at Harvard echoed his experience at Choate. Again, he felt himself to be in the shadow of his older brother Joe Jr., who was two years ahead of him and pegged as the most intelligent and driven of the Kennedy boys. JFK continued to make only lackluster grades–"gentleman's C's," as the expression went. He wrote occasionally for the Harvard Crimson, the campus newspaper, but had little involvement with campus politics, preferring to concentrate on athletics and his social life. He played football, and was on the JV squad during his sophomore year, but a bad fall led to a rupture of his spinal disc. The injury forced him off the team, and left him with back troubles that would plague him for the rest of his life. Off the field, in Harvard's social scene, he was more successful. He won membership in the Hasty Pudding Society and the Spee Club, one of Harvard's elite "final clubs," where bluebloods mingled and made the connections that kept America's aristocracy running. A contemporary called him "one of the most popular men in our class."

In 1937, while JFK was still in his sophomore year, Joseph Kennedy, Sr. was appointed Ambassador to Great Britain. This prestigious post opened new social avenues to the Kennedy family, and gave them front-row seats for the drama of World War II's approach. In the European theater, Adolf Hitler was preparing to occupy Austria and Czechoslovakia, and the British government was pursuing a policy of appeasement, designed to stave off war at all costs. As ambassador, Joseph Kennedy would staunchly support appeasing Hitler, and would be fiercely critical of Winston Churchill's calls for a stronger policy against the Nazi threat. History would not regard this impulse of Joseph Kennedy's to placate Germany any more kindly than future events would treat his strident anti-Semitism. "Never do business with Jews," he once told his sons, this bigotry ironic for a man who had himself been the victim of so much anti-religious sentiment, since he was Catholic.

In 1938, though, these concerns lay in the future, and JFK used his father's position to arrange a grand tour of sorts that would take him from France to Poland, down through Russia into the Mediterranean, and finally back up through Berlin and Paris, before bringing him home. He had made an earlier journey in the summer of 1937, and had returned very impressed with the organization and efficiency of the fascist states of Italy and Germany. This time, he arranged for his tour to count as a Harvard semester, and sailed for Europe in the winter of 1939, as Nazi tanks rolled into Czechoslovakia. Using his father's connections, JFK was able to stay in ambassadors' homes for the majority of his trip, and he sent detailed reports to Joe Sr. from every stop. JFK's most prescient observation came in Poland, where he noted that "rightly or wrongly the Poles will fight over the Question of Danzig," referring to the controversy over a Polish seaport that led to Hitler's invasion of Poland.

The tour lasted seven months, and ended with JFK back in London for the summer of 1939. He was still there when war broke out–over Danzig, as he had predicted–in September 1939. Germany invaded Poland, and Great Britain and France immediately declared war on Hitler's Reich. (America, as it had at the beginning of World War I, remained neutral.) Hitler's armies quickly crushed the Poles, and tensions at the French-German border immediately settled into a quiet stalemate–the so-called "phony war," which would last well into 1940.

JFK began his senior year at Harvard in the spring of 1940, with the campus buzzing over the events happening across the Atlantic. JFK showed more of an interest in politics now, joining the Crimson editorial board and penning a thesis on England's foreign policy before the war. The thesis was critical of Neville Chamberlain's lenient dealings with Hitler, but echoed Joe Sr.'s attitude in suggesting that the British people would not have accepted war before 1939, in any event. Entitled "Appeasement at Munich," it was well-received and helped JFK graduate magna cum laude, the second-highest possible ranking. More importantly, Joe Sr. seized upon the thesis as a way of making his JFK a public figure. Joe Sr. pulled strings in the publishing industry, hired a newspaper reporter to edit and polish the prose, and eventually had the thesis–retitled Why England Slept–published as a book in July of 1940. It was a modest best-seller, and gave JFK his first taste of celebrity.

With Harvard behind him, JFK briefly attended Stanford Business School, and, along with most Americans of his age, registered for the draft, in October 1940. His number was called, but he used his status as a student to defer entry into the military until summer 1941. Meanwhile, he left Stanford and took a rather aimless trip through South America in the spring of 1941. At this time, he was dating a number of women, a pattern that would continue throughout his life, even during his marriage. His health problems persisted, as well. He had stomach trouble, was far too thin, and failed physicals for both the army and the navy. But again, his father's connections prevailed, and a friendly doctor gave JFK a clean bill of health. JFK was sworn in as a naval ensign on September 25, 1941, less than two months before the bombing of Pearl Harbor would drag America into World War II.

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