Tenure
In 1989, on the 25th anniversary of the murder of the civil rights activists James Chaney, Andrew Goodman, and Michael Schwerner, Lott and the rest of the Mississippi congressional delegation refused to vote for the non-binding resolution honoring the three men which nevertheless passed the Congress.
Along with John Ashcroft, Larry Craig, and Jim Jeffords, Lott was a part of a group of Senators who sang as a barbershop quartet. Lott sang bass. The senators sang "Elvira" at the 1996 Republican National Convention.
He became Senate Majority Whip when the Republicans took control of the Senate in 1995. In June 1996, he ran for the post of Senate Majority Leader to succeed Republican Bob Dole, who had resigned from the Senate to concentrate on his presidential campaign. Lott faced his Mississippi colleague Thad Cochran, the then-Chairman of the Senate Republican Conference. Cochran cast himself as an "institutionalist" and who would help to rebuild public trust in Congress through compromise over conflict. Lott promised a "more aggressive" style of leadership and courted the younger Senate conservatives. Lott won by 44 votes to 8. As majority leader, Lott had a major role in the Senate trial following the impeachment of President Bill Clinton. After the House narrowly voted to impeach Clinton, Lott proceeded with the Senate trial in early 1999, despite criticisms that Republicans were far short of the two-thirds majority required under the Constitution to convict Clinton and remove him from office.
Lott generally pursued a conservative position in politics and was a noted social conservative. For instance, in 1998, Lott caused some controversy in Congress when as a guest on the Armstrong Williams television show, he equated homosexuality with alcoholism, kleptomania and sex addiction. When Williams, a conservative talk show host, asked Lott whether homosexuality is a sin, Lott simply replied, "Yes, it is."
According to the Anti-Defamation League, Lott was a frequent speaker at the white supremacist group Council of Conservative Citizens. Although he denied knowing of the group's intentions, it was later revealed members of his family had CCC membership.
After the 2000 elections produced a 50–50 partisan split in the Senate, Vice President Al Gore's tie-breaking vote gave the Democrats the majority from January 3 to 20, 2001, when George W. Bush took office and Vice President Dick Cheney's tie-breaking vote gave the Republicans the majority once again. Later in 2001, he became Senate Minority Leader again after Vermont senator Jim Jeffords became an independent and caucused with the Democrats, allowing them to regain the majority. He was due to become majority leader again in early 2003 after Republican gains in the November 2002 elections.
In 2003, Lott coined the term "nuclear option".
Lott spoke on December 5, 2002, at the 100th birthday party of Senator Strom Thurmond of South Carolina, a retiring Republican senator who had switched parties from the Democrats decades earlier. Thurmond had run for President of the United States in 1948 on the Dixiecrat (or States' Rights Democratic) ticket. Lott said: "When Strom Thurmond ran for president, we voted for him. We're proud of it. And if the rest of the country had followed our lead, we wouldn't have had all these problems over all these years, either."
As a senator and presidential candidate, Thurmond maintained an explicit States' Rights platform that challenged the Civil Rights Movement and later, the Civil Rights Act as illegally overturning the separation of powers under the United States Constitution and called for the preservation of racial segregation. The Washington Post reported that Lott had made similar comments about Thurmond's candidacy in a 1980 rally. Lott gave an interview to BET explaining himself and repudiating Thurmond's former views.
In the wake of the controversy, Lott resigned as Senate Republican Leader on December 20, 2002, effective at the start of the next session, January 3, 2003. Bill Frist of Tennessee was later elected to the leadership position. In the book Free Culture, Lawrence Lessig argues that Lott's resignation would not have occurred had it not been for the effect of internet blogs. He says that though the story "disappear[ed] from the mainstream press within forty-eight hours", "bloggers kept researching the story" until, "finally, the story broke back into the mainstream press." The New York Times, however, attributed his resignation to "ruthless maneuvering" by Karl Rove and George W. Bush to depose Lott, "a threat to the president’s agenda", and replace him with Frist, who had "long been the president's choice."
After losing the Majority Leader post, Lott was less visible on the national scene, although he did break with some standard conservative positions. He battled with Bush over military base closures in his home state. He showed support for passenger rail initiatives, notably his 2006 bipartisan introduction, with Sen. Frank Lautenberg of New Jersey, of legislation to provide 80 percent federal matching grants to intercity rail and guarantee adequate funding for Amtrak. On July 18, 2006, Lott voted with 19 Republican senators for the Stem Cell Research Enhancement Act to lift restrictions on federal funding for the research. On November 15, 2006, Lott regained a leadership position in the Senate, when he was named Minority Whip after defeating Lamar Alexander of Tennessee 25–24.
Senator John E. Sununu (R) of New Hampshire said, after Lott's election as Senate Minority Whip, "He understands the rules. He's a strong negotiator." Former House Speaker Newt Gingrich (R) said he's "the smartest legislative politician I've ever met."
Lott faced no Republican opposition in his primary race. State representative Erik R. Fleming placed first of four candidates in the June Democratic primary, but did not receive the 50 percent of the vote required to earn the party's nomination. Fleming and the second-place finisher, business consultant Bill Bowlin, faced off in a runoff on June 27, which Fleming won with 65% of the vote. Fleming criticized Lott for not doing enough to alleviate poverty in "the poorest state in the nation." Fleming's bid was viewed as a longshot, and Lott handily defeated him with 64% of the vote in November. Meanwhile, Sen. Rick Santorum of Pennsylvania lost his seat, opening up the job of assistant Republican leader, and Lott defeated Lamar Alexander of Tennessee 25-24 for the job.
On November 26, 2007, Lott announced that he would resign his Senate seat by the end of 2007. According to CNN, his resignation was at least partly due to the Honest Leadership and Open Government Act, which forbade lawmakers from lobbying for two years after leaving office. Those who left by the end of 2007 were covered by the previous law, which he cosponsored and which required a wait of only one year. In an interview regarding his resignation, Lott said that the new law "didn't have a big role" in his decision to resign.
Lott's resignation became effective at 11:30 p.m. on December 18, 2007. On January 7, 2008, it was announced that Lott and former Senator John Breaux of Louisiana, a Democrat, opened their lobbying firm about a block from the White House.