In the 1806 election the Republicans secured a majority in the Massachusetts assembly, and the gubernatorial election was notably close. Running mainly against James Sullivan, Strong barely received a majority of the votes cast. With fewer than 200 votes in the balance, the Republican-controlled legislature scrutinized the returns in a partisan manner, discarding ballots that had misspelled Strong's name while retaining those that misspelled Sullivan's and performing tallies in ways that favored their candidate. This process concluded with a finding that Strong in fact lacked a majority of votes, which was what was then required to carry the election, as opposed to the modern plurality requirement. Strong's Federalist allies in the legislature were able to publicize the partisan nature of the analysis, resulting in a hostile public backlash. He was proclaimed the winner after further, less biased, analysis corrected the count in his favor. However, in the 1807 election the rising tide of Republicanism swept Strong (along with other New England Federalists) out of office. Federalists asked him to run in 1808, but he refused, noting that he had "done his part" and that his home base in Hampshire County was strongly Federalist.