President of the Senate, 2000–2012
On January 5, 2000, Larry Saunders' promised resignation became official, and Williams was elected President of the Senate. The transition was generally regarded as cordial and smooth, although Democratic minority leader David Karem asked that the Senate journal reflect that the shift in majority was due to party defection, not a vote of the people. Democrats were also upset that Williams removed a minority seat from the powerful rules committee, giving the majority party a 5–3 advantage in representation. Williams defended the move, saying it was a return to the traditional composition of the committee; a 5–4 split between the majority and minority was part of a deal brokered with Saunders by Republicans for the 1998 session only, Williams said.
Williams and Democratic Speaker of the House Jody Richards both criticized Governor Patton early in the legislative session for presenting his budget and plan for tax reform to the legislature as a single package, rather than separately, as had been customary for previous governors. Elements of the tax plan – in particular, a seven-cent-per-gallon hike in the gasoline tax – were considered unlikely to pass in isolation, and Williams and Richards believed Patton had bundled the budget and tax plan in order to make it harder for legislators to oppose these elements. Senate Republicans remained firmly against enacting any new taxes for most of the session, hampering the General Assembly's ability to pass a bundled budget. Williams was able to hold his caucus together against tax increases until the last few days of the session, when they acquiesced on enacting a six percent tax on out-of-state phone calls. Still, Republicans claimed victory for having defeated Patton's larger tax plan.
During the session, Williams also forcefully criticized Patton for trying to reverse elements of a workers' compensation reform package Patton had passed during his first term and opposed a Democrat-backed plan for distributing federal money from the Tobacco Master Settlement Agreement to county governments instead of allowing the state government to allocate it toward a centralized plan for reducing the state's dependence on tobacco. Late in the session, Williams accused Patton of approaching two unnamed Republican senators and asking them to vote with the Democratic caucus to oust him as Senate president. Patton acknowledged meeting with "more than two" Republican senators, but insisted that the legislators had initiated the meetings to express their displeasure with Williams' leadership and that he never asked them to help oust Williams. After the session, and in the lead-up to the 2000 legislative elections, the strained relationship between Patton and Williams deteriorated when Patton said Williams had pledged to help him pass his proposed gasoline tax increase at a meeting at the Governor's Mansion in December 1999. Patton claimed Williams had made a list of Republican senators who would support the increase, those who would oppose it, and those who might be persuaded to support it. Williams denied that he ever pledged to help pass the tax and claimed Patton might have been mistaken regarding the details of their December meeting because, during the meeting, he was "drinking liquor and talking big." "He wasn't falling down drunk. He was mouthy drunk," Williams said. The fractured relationship between Patton and Williams endured for the remainder of Patton's term in office.
In the 2000 legislative elections, Republicans maintained their 20–18 advantage in the Senate. Previously limited to 60-day meetings in even-numbered years, the Kentucky General Assembly was allowed a 30-day session in odd-numbered years by a constitutional amendment passed in 2000. As the 2001 session opened, the Republican-controlled Senate and Democrat-controlled House clashed over the makeup of joint committees that meet in the interim between legislative sessions to study issues and draft legislation for the upcoming session. Senate Republicans called for equal representation on the committees to reflect their control of that chamber; Democrats insisted that, because the House had more members, the House should be represented by more members on the joint committees. Late in the session, Williams introduced a proposal to the bipartisan Legislative Research Commission – which was made up of eight Democrats and eight Republicans – that would have allowed each chamber to name their own members to the joint interim committees, helping to resolve the parity issue. The vote was an 8–8 tie along strict party lines, and the issue remained unresolved. The disagreements over committee parity dominated the session, which counted legislation to clean up brownfield land, to outlaw racial profiling in police departments receiving state aid, and to designate the Appalachian dulcimer as the state's official musical instrument among its few accomplishments. In July 2001, Williams and House Speaker Jody Richards reached an agreement to allow committees of four representatives and three senators to meet up to three times in advance of the 2002 legislative session.
One of the items left unaddressed in the 2001 legislative session was approving a redistricting plan for the state based on the 2000 Census. Republicans advocated for Governor Patton to call a special legislative session following the 2001 regular session for the purpose of considering redistricting, but Patton refused to call such a session unless House and Senate leaders had an agreed-upon plan in place first. Republicans charged that Patton was intentionally delaying the redistricting so that the 2002 legislative elections would take place with districts drawn by the Democrat-controlled General Assembly a decade earlier to favor Democratic candidates. Patton denied that charge. In September 2001, a group of Democratic senators claimed that the official census figures underrepresented the state's population by approximately 50,000 people, especially minorities, children, and the homeless. They asked that the Census Bureau release scientifically adjusted figures that would account for those underrepresented populations. Williams decried this request as another attempt by Democrats to forestall the redistricting debate until after the 2002 elections. In October 2001, the Census Bureau announced that it believed the adjusted figures were unreliable and refused to release them.
In the opening days of the 2002 General Assembly, House Democrats angered Senate Republicans by submitting maps of proposed districts for the House and Senate. Previously, each chamber had only submitted maps for its own districts. During the ensuing negotiations, Williams promised that Senate Republicans would vote for any redistricting plan the House devised for its districts if House Democrats would agree to do the same for the Senate, but House Speaker Jody Richards refused. After weeks of negotiations, the Assembly approved a plan that gave House Democrats most of what they wanted with regard to House districts and Senate Republicans most of what they wanted with regard to Senate districts. After Senate Democrats complained about the bill, House Majority Leader Greg Stumbo chided them for "not [accepting] the fact that 20-18 means Republicans control the Senate" and encouraged them to campaign hard to win back the chamber in future elections.
Williams remained President of the Senate until November 2012, being re-elected to represent his Senate district in November 2002, November 2006, and November 2010. In 2009, he announced that he would remain in the state Senate and not challenge incumbent Jim Bunning in the 2010 Republican senatorial primary. Bunning later announced that he would not seek reelection to a third term.