Mogae was seen by many to be a compromise successor to Masire, whose tenure was, in later years, marked by dissension within the BDP ranks. Masire's decision to step down and allow Mogae to take over the presidency can be viewed as an indication of his confidence that Mogae would be able to mend the rift in the party prior to 1999 elections. This was a significant challenge facing Mogae in the period prior to those elections, since the party had split in two, with a division between the moderate and conservative factions of the leadership. Shortly after his inauguration, Mogae reshuffled his cabinet and reassigned leaders of the factions to portfolios designed to keep them more involved in government issues, with less time to pursue activities that erode party unity. Many observers expected Mogae to select one of the two faction leaders as his vice president, but instead, in a move that many viewed as politically shrewd, he named Lt. General Ian Khama to that post. Khama is popular in his own right and is the son of Botswana's first president. He is respected by both party factions and brings with him the grassroots support that Mogae himself lacks.
Eighteen months later, Mogae's party, the BDP, won 33 of the 40 parliamentary seats in the general elections held on 16 October 1999. The remaining seats went to the Botswana National Party (six seats) and the Botswana Congress Party
(one seat). Festus Mogae was inaugurated as president based on the landslide win of his party in these elections.
Mogae came to the presidency with ample government experience, having the distinction of serving under both of the country's post-independence presidents. Even prior to assuming presidential powers, Mogae indicated that he would concentrate on implementing policies of his predecessor, especially those targeting job creation and poverty, with just a few refinements. Thus it is unlikely that Mogae's administration will herald a significant departure from that of Masire.
Precisely because Botswana's democracy is stable, the likelihood of political crisis is remote. Political issues that have the potential to paralyze or destroy other African governments are readily handled by the democratic institutions that have developed in Botswana. Thus Mogae should be able to devote a significant amount of attention to retaining the BDP leadership.