By 1899, the Republicans were back in the majority in the General Assembly and another U.S. Senate seat came vacant. In 1901, the second one became vacant as well. Now Delaware had two seats vacant and still the General Assembly could not elect anyone. The situation was drawing national attention, and ridicule. Finally, the "Regular Republicans" issued an ultimatum to Allee, saying they would cooperate with the Democrats unless Addicks would relent. Under much pressure, Addicks did finally compromise by allowing his lieutenant, Allee, to be elected to one of the U.S. Senate seats on March 2, 1903. By the time Allee's term ended, Addicks had lost his fortune and left Delaware politics.
T. Coleman du Pont became the effective Republican leader and managed to bring the two competing factions together. Without his mentor, Allee was politically stranded, and therefore, was not a candidate for reelection when his term ended. Allee filled the vacancy in the term commencing March 4, 1901. During this term, he served with the Republican majority in the 58th and 59th Congress. In the 58th Congress he was Chairman of the
Committee on Indian Depredations until December 14, 1904, when he left the committee to become chairman of the Committee on the Organization, Conduct, and Expenditures of the Executive Departments. During the 59th Congress, he chaired the
Committee on Railroads. In all, he served from March 2, 1903, until March 4, 1907, during the administration of U.S. President Theodore Roosevelt. Years later, Allee became involved with yet another Republican intra-party squabble. This grew out of the bitter competition between
Alfred I. du Pont and
Pierre S. du Pont. Allee gave his support to
Alfred I. du Pont. ==Death and legacy==