In 2006, Guterres attempted to take over the leadership of FRETILIN from Mari Alkatiri, the party's Secretary-General, but Alkatiri prevailed at a FRETILIN national congress.
After Indonesia invaded the nascent nation on December 7, 1975, Alkatiri and his colleagues were unable to return, and he established the headquarters of the FRETILIN External Delegation in Maputo, Mozambique.
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In the June 2007 parliamentary election, Alkatiri was re-elected to a seat in parliament; he was the second name on FRETILIN's candidate list, after party president Francisco "Lu Olo" Guterres.
Separatist movements operating in Indonesia, such as the Darul Islam (Indonesia), Fretilin (East Timorese independence militia during Indonesian occupation of East Timor), Gerakan Aceh Merdeka, and Organisasi Papua Merdeka are often held responsible on terrorist attacks, such as bombings and shootings, in Indonesia.