The IPA was inaugurated in late 1998 and immediately became embroiled in contentious debate regarding the type of electoral system to embrace. Eventually there was an agreement to change the structure of the lower house of parliament, the National Assembly: of 120 seats, 80 would be directly elected, and the remaining 40 would be indirectly elected, allocated to qualifying political parties on the basis of proportional representation. Reaching an agreement took longer than expected, though, and the IPA was not able to establish an electoral schedule in time for elections to be held in 2000. In 2002, when the elections were finally held, the LCD again emerged with the majority of parliamentary seats, and Mosisili was named to a second term as prime minister. In 2006, dissension within the LCD resulted in one of the party’s prominent ministers, Motsoahae Thomas Thabane, leaving to form the All Basotho Convention (ABC); many other LCD ministers followed Thabane to the ABC. Nevertheless, the LCD managed to maintain control of the parliament after early elections were called in February 2007. Although the elections were generally viewed as free and fair by international observers, the ABC and other parties contested the way that the proportional seats had been allocated. Mediation efforts continued for several years before resulting in a resolution that was agreed upon by all of Lesotho’s parties in 2011.

Meanwhile, local government elections were held in 2005—the first such elections since independence—but were clouded by low voter turnout (less than one-third of eligible voters participated). Later that year the government made an ambitious effort to address the country’s growing HIV/AIDS pandemic by offering free HIV testing to the entire population. Although the objective was to reach every household by the end of 2007, the program fell short of its goal, stymied by such factors as a lack of necessary medical staff and the logistics of reaching the many rural and mountainous locations in the country.

Lesotho also faced other problems in the early 21st century. The continued decline in agricultural production—caused in part by endemic soil erosion in the already limited arable land as well as by repeated droughts and the impact of the HIV/AIDS pandemic on the workforce—resulted in chronic food shortages, and widespread poverty and unemployment plagued the country.

In early 2012, further dissent within the LCD led to Mosisili leaving the party and establishing the Democratic Congress (DC), which then became the ruling party. When parliamentary elections were held later that year in May, the DC won more seats than any one party, but it did not win an outright majority and was unable to form a governing coalition. A coalition assembled by Thabane’s ABC, which included the LCD, then gained majority control of the National Assembly. Mosisili resigned as prime minister and was succeeded by Thabane; Mothetjoa Metsing, head of the LCD, was named deputy prime minister.

The coalition was tenuous but held together in 2013 before beginning to unravel the next year, with Thabane being accused by his coalition partners of having not conferred with them before taking action on a number of occasions. In June 2014, faced with the likelihood of a no-confidence vote, Thabane suspended parliament, angering the other coalition members. Later that month SADC officials began attempts to broker an agreement between the parties, but no immediate solution was reached.

Tensions in the country reached a boiling point in late August 2014, shortly after Thabane fired the head of the army, Lieut. Gen. Kennedy Tlali Kamoli. Kamoli refused to step down and instead on August 30 led a number of military troops in seizing police stations and television and radio facilities as well as surrounding the residence of Thabane, who fled to South Africa. Soldiers also disarmed the country’s police force, which was generally viewed as being supportive of Thabane; the military claimed to be acting on intelligence that the police were planning to supply weapons to protestors ahead of an upcoming demonstration. An emergency meeting on September 1 between Thabane, Metsing, and SADC leaders led to an agreement for Thabane to return to Lesotho, for parliament to be reconvened, and for SADC observers to be stationed in the country. The next round of parliamentary elections, which had been scheduled for 2017, were moved up to early 2015 in the hope of forming a more stable government. However, no party won an outright majority of seats in the February 28 election. Thabane’s ABC won more of the 80 elected seats than any other party, but, after the 40 seats reserved for proportional representation were distributed, Mosisili’s DC party narrowly finished with the most seats. Mosisili formed a coalition with several smaller parties and was inaugurated as prime minister on March 17.

The early elections and subsequent new government did not completely ease the political tensions in the country. Thabane and other opposition leaders continued to live in exile, citing concerns for their safety, and Kamoli remained in place as head of the armed forces, in spite of his controversial actions and calls for him to step down by the SADC and others. In an effort to foster greater political stability, the SADC worked with the government on the creation and implementation of reforms to Lesotho’s security and public sectors as well as to the country’s constitution. One of the SADC’s recommendations was acted on in late 2016, when Kamoli finally agreed to step down and retired from the armed forces.

Thabane and two other opposition leaders returned to Lesotho in February 2017, leading a coalition to challenge Mosisili. When parliament convened later that month, Mosisili lost a vote of confidence. In March King Letsie dissolved parliament and called for a general election to be held on June 3, 2017. Thabane’s ABC won 47 of the 80 elected seats; Mosisili’s DC party won 26 seats. After the 40 seats reserved for proportional representation were distributed, the ABC had a total of 48 seats—more than any other party, but short of a majority—and the DC had 30. Thabane announced the formation of a governing coalition with three other parties, and Mosisili, accepting the election results, resigned.

News surfaced in January 2020 that the police were investigating Thabane and his current wife, Maesaiah, in connection with the June 2017 murder of his estranged wife, Lipolelo, leading ABC leaders to call for his immediate resignation. Although Thabane agreed to resign, he would not agree to do so immediately. He later said that he would step down by the end of July, but calls for him to resign sooner than that continued. Meanwhile, in February Maesaiah was charged in Lipolelo’s murder.

As Thabane continued to face calls for his resignation as well as a threatened vote of no confidence, in March the National Assembly passed a bill proposing a constitutional amendment that would limit the prime minister’s ability to dissolve parliament and to call for new elections, especially if a vote of no confidence had been passed or if the prime minister was advising the king to dissolve parliament. But before the bill could be passed by the Senate and approved by the king, Thabane suspended parliament for three months, ostensibly because of the COVID-19 global pandemic. His suspension order, however, was overturned on April 17 by the Constitutional Court. The amendment bill was then passed by the Senate and approved by the king, and the constitution was amended in early May, limiting Thabane’s options in the ongoing political crisis. Thabane’s ruling coalition collapsed on May 11, and he formally resigned on May 19, 2020. His finance minister, Moeketsi Majoro, was sworn in as prime minister the next day.

In November 2021, Thabane was charged in connection with the 2017 murder of his estranged wife, just as his current wife, Maesaiah, had been charged the previous year. However, charges against both Thabanes were dropped in July 2022 after prosecutors were unable to locate a key witness in the matter.