In the first years after the Indonesian Anschluss, Nicolau Lobato rose to the status of undisputed leader of the Timorese Resistance, replacing the controversial first President of the Republic proclaimed on 28 November 1975, Francisco Xavier do Amaral. After Nicolau was shot dead on the last day of December 1978, a few years elapsed before Xanana could rise to a similar position in the Conference of March 1981. Xanana's leadership started inside one political party (FRETILIN) and its armed branch (FALINTIL), but slowly grew beyond those frontiers to embrace emerging sectors of the population that were increasingly turning against Indonesian domination. By the end of the 1980s, Xanana's position had evolved: severing his ties with his political party and declaring the guerrilla force he commanded as a liberation army of the entire Resistance organized under the umbrella of CNRM (Conselho Nacional da Resistência Maubere [National Council of Maubere Resistance]), Xanana moved from a position of ‘revolutionary’ leader to one of ‘nationalist’ leader. This was to survive his imprisonment in 1992, and would be made even more explicit in 1998 when all branches of the Resistance upgraded their joint efforts to combat Indonesian occupation creating the National Council of Timorese Resistance (CNRT) whose presidency was awarded to Xanana, by then a political prisoner in Cipinang. The moral authority of the guerrilla fighter who had spent 17 years in the Timorese mountains was thus recognized by all the relevant players in the struggle for self-determination (Niner 2009; Feijó 2016a).

The existence of a strong, popular and charismatic leader would suggest that the political institutions to be designed once the road to full independence was inaugurated with the Referendum of 30 August 1999 would accommodate a prominent executive function to be vested upon Xanana. Similar cases of postcolonialism, including all the former Portuguese domains in Africa, had adopted regimes in which a strong president was a critical feature. However, the Timorese situation was far more complex as the nationalist movement was plural, encompassing organizations with different historical trajectories, and diverse personalities with deep-rooted rivalries. The relationships between Xanana and the various organizations under the umbrella of CNRT were differentiated, and old animosities persisted between himself and many in commanding positions of FRETILIN, by and large the best structured of all the political organizations, with considerable popular support of its own.