On the domestic front, President Roosevelt was one of the most visible Progressives of his time. Many of his domestic policies involved fighting big industry and corruption in an attempt to help the common man. He offered the American people a Square Deal to improve their standard of living and exert more control over large domineering corporations or trusts. Trusts, which were technically illegal under the 1890 Sherman Act, attempted to consolidate business interests to create a monopoly on specific products and eliminate competition. Many businesses attacked Roosevelt as a socialist, but he ardently refuted these accusations and refuted the principles of Marxism. In truth, Roosevelt did not despise big business, and in fact realized that the trusts had indirectly increased the standard of living for nearly every American in the latter half of the nineteenth century. Roosevelt did, however, dislike the power of the trusts and the fact that the American public had little control of them. On the other hand, however, he also feared giving too much power to labor. His Square Deal policies attempted to strike a balance between the two.

Roosevelt's first major domestic test as President came when 140,000 miners in eastern Pennsylvania went on strike in the 1902 Coal Strike. Coal was a vital energy source for almost all Americans during this era, and the nation panicked during the strike. Represented by John Mitchell, the miners formed the United Mine Workers Union to demand higher wages and better working conditions. The president of the Philadelphia and Reading Railroad Company and owner of the mine, George Baer, would not concede to the strikers' demands. Mitchell approached Roosevelt and asked him to establish an independent arbitration council. Baer–and, ironically, even the miners themselves–refused arbitration. Roosevelt, under pressure from Republicans and the American citizenry and not even considering the legality of his actions, planned to replace the strikers by force with ten thousand Army troops and begin mining coal again if a settlement could not be reached. Fortunately, Secretary of War Elihu Root was able to avert a disaster. Working with banker J.P. Morgan, Root was able to convince the miners to accept independent arbitration. Roosevelt won the American people's approval of the way he handled the situation.

Also in 1902, President Roosevelt shocked financiers on Wall Street with his decision to approve the government's lawsuit against Northern Securities, a large and recently merged western railroad company, for violating the Sherman Anti-Trust Act. J.P. Morgan, the financier who had arranged the merger and who had significant amounts of money invested in Northern Securities, took Roosevelt's decision as a personal insult. Many conservative Republicans in Congress and bankers on Wall Street attacked the President and Attorney General Philander Knox for the decision. The American people, one the other hand, loved Roosevelt for his boldness in the face of the trusts. To ensure the government's victory, Roosevelt also nominated Oliver Wendell Holmes, Jr., to replace Justice Horace Gray on the Supreme Court. As Chief Justice of the Massachusetts Supreme Court, Holmes had voted against industry and railroads in similar suits, making him the perfect choice from Roosevelt's perspective. In the end, the U.S. government won the suit, Northern Securities was dismantled into smaller companies, and President Roosevelt came to be known as the "Trustbuster."

As the Sherman Act had never been truly enforced until this time, the breakup of Northern Securities opened the floodgate for suits against other major trusts. Famous among these was Roosevelt's "busting" of the Standard Oil trust. Muckraker Ida Tarbell's History of Standard Oil, which was published in McClure magazine, detailed the business practices of Rockefeller's oil machine. Tarbell accused Standard Oil of issuing rebates in total of one million dollars to its customers to effectively eliminate competition. In 1906, Roosevelt had the Hepburn Bill drafted and passed through Congress to reform rate evaluations and outlaw excessive rebates designed to thwart competitors. The bill also stipulated that all companies engaged in interstate commerce were under the supervision of the federal government. The bill hurt not only Standard Oil but the powerful rebate-issuing railroads as well. In all, Roosevelt brought lawsuits against forty-three other trusts during his Presidency.

In 1907, financial troubles hit the United States when the Knickerbocker Trust Company in New York failed, leading to a cascade effect that caused many other banks to totter as well. Conservative Republicans blamed Roosevelt for the economic distress, claiming that his actions had undermined stability and shattered consumer confidence. Roosevelt shot back that it was the plutocracy that caused the troubles. Although it was impossible to discern at the time, the rest of the world was suffering as well, and the Panic of 1907 was neither the result of Roosevelt's policies or the plutocrats' business practices. When the large brokerage of Moore and Schley nearly collapsed, J.P. Morgan once again met with the President. Moore and Schley held five million dollars of stock in the Tennessee Coal and Iron Company that it could not convert to cash to pay its investors. Morgan suggested that financially sound U.S. Steel Company purchase the Tennessee Coal and Iron Company, validating its stock, and thus stabilize Moore and Schley. This plan would work so long as Roosevelt approved the merger and promised not to declare it a violation of the Sherman Act. Roosevelt consented, U.S. Steel purchased Tennessee Coal and Iron, and as a result the stock market did not collapse. Together, Roosevelt and Morgan successfully avoided a widespread economic depression.

Upton Sinclair's 1906 novel The Jungle, which graphically depicted the horrible working conditions of the Chicago stockyards and meatpacking industry, spurred Roosevelt to make other reforms. The President was especially disgusted by Sinclair's apparently fact-based account of a machinist who fell into a meat grinder and emerged as canned meat to be sold and eaten. Roosevelt called for immediate action and organized an investigation into the packinghouses in Chicago and other cities. The details of the report turned out to be not far from Sinclair's fictional account. An outraged public cry for action quickly produced the Meat Inspection Bill and later the creation of the Food and Drug Administration.

Another major component of Roosevelt's domestic policy was conservation, stemming from his great love of the outdoors. After having toured the nation on several campaign trips, including stints in California, the Pacific Northwest, and the Southwest, the president determined to conserve as much land as possible. Roosevelt's idea of conservation was groundbreaking–at the time, the idea of conserving the land primarily meant not preservation, but merely saving the land for future generations to use later. For this reason, most of the conserved land at that point was forest that provided valuable timber. During his administrations, Roosevelt purchased 150 acres of land to conserve. Roosevelt also consorted with many prominent conservationists of the time, such as Gifford Pinchot and John Muir, and established many wildlife preservations along with them. The National Forest Service was organized and additional National Parks were set aside throughout the U.S. for recreation and conservation purposes. Such acts faced opposition from many members of Congress and Western settlers who had plans to use the land that was being set aside. Settlers were, however, pleased with the 1902 Reclamation Act that set aside money to irrigate previously dry and unlivable tracts of land.

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