In 2005 and early 2006, Vakatora spearheaded moves to forge an electoral alliance among indigenous Fijian-led political parties ahead of parliamentary elections held on 6–13 May 2006.
Vakatora's calls were immediately rejected by Opposition Leader Mahendra Chaudhry, who said that Indo-Fijians were already underrepresented, claiming that they had given up two seats in the constitutional revision of 1997 in order to make way for the minority groups.
In his last years, when not addressing politics at the national level, Vakatora spent time advising Rewan villagers on the controversial Qoliqoli Bill and how it would affect them.
Vakatora's autobiography, From the Mangrove Swamps, tells of his life as a simple village boy who enjoyed catching mud crabs, to his rise to the corridors of power, as a senior civil servant, a government minister, and Speaker of Parliament.
Akuila Yabaki (a close personal friend, despite political differences) described Vakatora, the son of a Methodist minister, as a committed Christian whose life was characterized by weekly prayer meetings in his home.