Second term (2001–2006)
In 2001, Museveni won the presidential elections by a substantial majority, with his former friend and personal physician Kizza Besigye as the only real challenger. Museveni had 5,088,470 votes, which stood at 69.4%, followed by his counterpart Besigye, who got 2,029,190 votes standing at 27.7%. The total number of voters who registered were 10,775,836 out of which only 7,511,606 voted with total vaild votes of 7,327,079 and invalid votes of 184,527. The leading district in voting was Kamwenge in which 111,146 voters voted and 110,188 voters were valid standing at 92.1%. In a populist publicity stunt, Museveni travelled on a bodaboda motorcycle taxi to submit his nomination form for the election.
There was recrimination and bitterness during the 2001 presidential elections campaign, and incidents of violence occurred following the announcement of the win by Museveni. Besigye challenged the election results in the Supreme Court of Uganda. Two of the five judges concluded that there were such illegalities in the elections and that the results should be rejected. The other three decided that the illegalities did not affect the result of the election in a substantial manner, but stated that "there was evidence that in a significant number of polling stations there was cheating" and that in some areas of the country, "the principle of free and fair election was compromised."
Besigye had been a close confidant of the president and was his physician during the Ugandan Bush War. They had a terrible fallout shortly before the 2001 elections, when Besigye decided to stand for the presidency. The 2001 election campaigns were a heated affair, with Museveni threatening to put his rival "six feet under".
After the elections, political forces allied to Museveni began a campaign to loosen constitutional limits on the presidential term, allowing him to stand for election again in 2006. The 1995 Ugandan constitution provided for a two-term limit on the tenure of the president.
Moves to alter the constitution and alleged attempts to suppress opposition political forces have attracted criticism from domestic commentators, the international community, and Uganda's aid donors. In a press release, the main opposition party, the Forum for Democratic Change (FDC), accused Museveni of engaging in a "life presidency project", and for bribing members of parliament to vote against constitutional amendments, FDC leaders claimed:
The country is polarized with many Ugandans objecting to [the constitutional amendments]. If Parliament goes ahead and removes term limits, this may cause serious unrest, political strife and may lead to turmoil both through the transition period and thereafter ... We would therefore like to appeal to President Museveni to respect himself, the people who elected him, and the Constitution under which he was voted President in 2001 when he promised the country and the world at large to hand over power peacefully and in an orderly manner at the end of his second and last term. Otherwise, his insistence to stand again will expose him as a consummate liar and the biggest political fraudster this country has ever known.
As observed by some political commentators, including Wafula Oguttu, Museveni had previously stated that he considered the idea of clinging to office for "15 or more" years ill-advised. Comments by the Irish anti-poverty campaigner Bob Geldof sparked a protest by Museveni supporters outside the British High Commission in Kampala. "Get a grip Museveni. Your time is up, go away", said Geldof in March 2005, explaining that moves to change the constitution were compromising Museveni's record against fighting poverty and HIV/AIDS.
In an opinion article in the Boston Globe and in a speech delivered at the Wilson Center, former US Ambassador to Uganda Johnnie Carson heaped more criticism on Museveni. Despite recognizing the president as a "genuine reformer" whose "leadership [has] led to stability and growth", Carson also said, "we may be looking at another Mugabe and Zimbabwe in the making". "Many observers see Museveni's efforts to amend the constitution as a re-run of a common problem that afflicts many African leaders – an unwillingness to follow constitutional norms and give up power".
In July 2005, Norway became the third European country in as many months to announce symbolic cutbacks in foreign aid to Uganda in response to political leadership in the country. The UK and Ireland made similar moves in May. "Our foreign ministry wanted to highlight two issues: the changing of the constitution to lift term limits, and problems with opening the political space, human rights and corruption", said Norwegian Ambassador Tore Gjos. Of particular significance was the arrest of two opposition MPs from the FDC. Human rights campaigners charged that the arrests were politically motivated. Human Rights Watch stated that "the arrest of these opposition Members of Parliament smacks of political opportunism".
A confidential World Bank report leaked in May suggested that the international lender might cut its support to non-humanitarian programmes in Uganda. "We regret that we cannot be more positive about the present political situation in Uganda, especially given the country's admirable record through the late 1990s", said the paper. "The Government has largely failed to integrate the country's diverse peoples into a single political process that is viable over the long term... Perhaps most significant, the political trend-lines, as a result of the President's apparent determination to press for a third term, point downward."
Museveni responded to the mounting international pressure by accusing donors of interfering with domestic politics and using aid to manipulate poor countries. "Let the partners give advice and leave it to the country to decide ... [developed] countries must get out of the habit of trying to use aid to dictate the management of our countries." "The problem with those people is not the third term or fighting corruption or multiparters", added Museveni at a meeting with other African leaders, "the problem is that they want to keep us there without growing".
In July 2005, a constitutional referendum, which was won by pro-democracy forces lifted a 19-year de-facto ban on political parties. Before the vote, the FDC spokesperson stated, "Key sectors of the economy are headed by people from the president's home area... We have got the most sectarian regime in the history of the country in spite of the fact that there are no parties."
Many Ugandans saw Museveni's conversion to political pluralism as a concession to donors – aimed at softening the blow when he announces he wants to stay on for a third term. Opposition MP Omara Atubo has said Museveni's desire for change was merely "a façade behind which he is trying to hide ambitions to rule for life".
In September 2004, Museveni delivered the keynote address at the Ugandan North American Association (UNAA) convention in Seattle, Washington, accompanied by First Lady Janet Museveni and U.S. Congressman Jim McDermott.
On 30 July 2005, Sudanese vice-president John Garang was killed when the Ugandan presidential helicopter crashed while he was flying back to Sudan from talks in Uganda. Garang had been Sudan's vice-president for three weeks before his death. Widespread speculation as to the cause of the crash led Museveni, on 10 August, to threaten the closure of media outlets that published "conspiracy theories" about Garang's death. In a statement, Museveni claimed that the speculation was a threat to national security. "I will no longer tolerate a newspaper which is like a vulture. Any newspaper that plays around with regional security, I will not tolerate it – I will close it." The following day, popular radio station Kampala Frequency Modulation(KFM) had its license withdrawn for broadcasting a debate on Garang's death. Radio presenter Andrew Mwenda was eventually arrested for sedition in connection with comments made on his KFM talk show.
