In October 1886, Theodore Roosevelt returned to New York City and accepted the Republican nomination for Mayor. He opposed Democratic candidate Abram S. Hewitt and Labor Party candidate Henry George, a former printer and author with an extreme left-wing agenda the Republicans found distasteful. Not all Republicans supported Roosevelt, however. Some denounced him for holding reformist opinions similar to George's. Others felt that by voting for Roosevelt, the party would be divided and George would have a better chance of winning. To keep George out of office, these Republicans suggested voting for the Democrat Hewitt. Although Roosevelt accepted the nomination, he believed his chances of actually winning were slim to none. Nevertheless, he remained faithful to the wishes of the party and ran. He was badly defeated. In the end, many of the conservative Republicans opted for the safer route and voted for Hewitt, who won with over 90,000 votes. Roosevelt came in third with barely 60,000. Never having expected much, Roosevelt soon forgot about his bid for the mayoralty and rushed off to attend to more important matters. Right after losing, he sailed to England to marry Edith.

For a time it seemed as if Roosevelt's political career had ended; it also seemed his ranching days were finished. While he and Edith were honeymooning in Italy, a bitter cold spell destroyed nearly every head of cattle at the Elkhorn Ranch. Roosevelt returned home to Sagamore Hill to live a quiet life away from politics. He was unable to stay away for long, however. In 1888 Benjamin Harrison received the Republican Presidential nomination, and Roosevelt seized the opportunity to reenter public life and campaign for Harrison, hoping to gain his favor and perhaps be appointed to a political office should Harrison become President. When Harrison was elected, Roosevelt was given a post in the new government as head of the U.S. Civil Service Commission.

During this period in American politics, the civil service bureaucracy was little more than a gigantic spoils system. Men elected to be president would often grant offices to those who had in one way or another supported them during the campaign. Ironically, although Roosevelt had arguably been somewhat of a spoils-seeker himself during the Harrison campaign, he despised the system. Upon his appointment as Commissioner of the Civil Service, he immediately began making reforms, attacking the spoils system publicly and furiously. One of his more infamous investigations involved the new Postmaster General, John Wanamaker, who had allegedly appointed a good number of his personal friends as regional postmasters. Many, including even President Harrison, heavily criticized Roosevelt for the investigation. When Democrat Grover Cleveland was elected President in 1892, Roosevelt felt sure the new President would strip him of his position; yet, to his surprise, Cleveland asked Roosevelt to stay and continue reforming the Civil Service.

Theodore remained Civil Service Commissioner until 1895, when he returned to New York City and accepted a position as New York City Police Commissioner under the newly elected Republican mayor, William Strong. Here too, Roosevelt made a name for himself as a reformer. He fought Tammany Hall corruption when he began firing police officers, even veteran lieutenants and captains who had served long terms on the force. He promoted officers based on merit and chastised those who neglected their duties. Roosevelt became famous throughout New York–and even the rest of the U.S.–for keeping a watchful eye on his officers. He would even walk many of the beats himself in order to catch negligent patrolmen. As usual, however, Roosevelt also made many enemies as Commissioner. When he began enforcing an often-overlooked city ordinance requiring pubs and saloons to shut down on Sundays, he faced heavy fire from New Yorkers and the press. Roosevelt paid little attention, however. Within a year, he had begun to tire of the job as Police Commissioner and focused on a more promising event: the 1896 presidential election.

The Republican nomination for president in 1896 went to William McKinley, a conservative and wealthy man from the East. Roosevelt completely supported McKinley and vehemently spoke out against opposing candidate William Jennings Bryan. Mark Hanna, McKinley's political advisor, sent Roosevelt on a tour through the Midwest to speak on behalf of the Republican candidate. McKinley easily won the election and awarded Roosevelt the coveted and prestigious position of Assistant Secretary of the Navy.

Roosevelt eagerly seized this opportunity. He felt this was his chance to make policy, to increase national strength and exert American influence abroad. Much like he had in his A History of the Naval War of 1812, Roosevelt once again championed a strong navy and military, being prepared for war, and quick action against those who could possibly become rivals in the future. He desired fighting a war with the Spanish Empire, not only to liberate the enslaved Cubans, but also to expel the imperial Spanish from the Caribbean entirely. Although President McKinley was an imperialist, he did not share Roosevelt's desire for war. Roosevelt spent much of his time as Assistant Secretary trying to convince others in the government that war was indeed necessary. He also focused great energy on preparing the U.S. Navy for war. He even began planning battle strategies. When war was eventually declared in 1898, he was ready for any and all contingencies and took quick action.

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