On 14 November 1974, Lemos Pires was appointed by the new Portuguese Government as Governor and Commander-in-Chief of the overseas province of Portuguese Timor. Posted to what was thought to be one of the more peaceful Portuguese territories, Lemos Pires found himself in the middle of a brewing conflict in Timor, while charged by the government to prepare Timor for independence. One of his first decrees made upon his arrival in Dili was to legalise political parties in preparation for elections to a Constituent Assembly in 1976. In August 1975, one of those political parties, the Timorese Democratic Union staged a coup against the Portuguese administration, prompting the outbreak of a three-month civil war, with many UDT politicians and supporters fleeing across the border to West Timor in Indonesia, where they were required to sign a petition calling for East Timor's incorporation into Indonesia. As a result of the conflict, Lemos Pires ordered the withdrawal of the Portuguese administration to the island of Atauro, off Dili. With opinion at home becoming increasingly detached from political developments in Timor, and more concerned with decolonisation in its African colonies of Angola and Mozambique than with Timor, Lemos Pires' attempts to broker an agreement between the UDT and the other prominent Timorese party, FRETILIN, were undermined, even while he insisted that he was awaiting instructions from the government in Lisbon. Without any possibility of support from Portugal, Lemos Pires maintained his administration for three months until he ordered a withdrawal of staff and left his post for Lisbon on 27 November 1975. Less than two weeks later, on 7 December, Indonesia invaded East Timor, leading to a situation of Indonesian occupation that would last until 1999. At the 2003 Truth and Reconciliation Commission hearings held by East Timor, Lemos Pires explained his position at the time, as well as to why Portugal had failed to support Timor during the invasion: "We were so much more worried about what happened in Portugal than what happened in Timor. For example, they couldn't dispense forces - in good condition and with goodwill - to go to Timor to ensure security there. At the same time, for instance, we had no ambassador in Jakarta - and that was a very important post for us. And the political credibility of Portugal at that time was so low. Of course, if Portugal was prepared and had the force and political respect at that moment, we could have done better. The problem was that I became alone in that moment. Portugal forgot East Timor because on the one hand it was the revolution, on the other it was African decolonisation, and so many Portuguese there in such bad conditions."
Later life
On his return to Lisbon, he was appointed commander of the Training Center for Special Operations and lectured at the Institute for Advanced Military Studies, of which he was Deputy Director. Later rising to be chief of staff of the Ministry of National Defense and the Director of the National Defence College. In 1982 he was promoted to Major-general and ended his military career as secretary general of the study center EuroDefense-Portugal. After his military career, he was vice president of the Fraternal Aid to Mozambique and published a book about his experiences in Timor entitled: Decolonization of Timor: Mission impossible?.
