AC allied itself with the Bharatiya Janata Party (BJP) and was a founding member of the National Democratic Alliance.
Wangcha Rajkumar, who had been elected to the Lok Sabha from the constituency Arunachal East in both 1996 and 1998, accused Apang of resorting to nepotism when his son was appointed minister.
One reason, it claimed, that the AC-BJP combine fared so badly was that several armed factions especially the powerful National Socialist Council of Nagaland in the area worked against them.
Ahead of the 2004 Lok Sabha elections the political map of Arunachal Pradesh had been redrawn yet again.
Arunachal Congress did however continue to exist as a party even after that the founder Apang had joined BJP.
Ahead of the 2004 Lok Sabha elections AC talked about calling for a boycott, as a protest against that Chakma and Hajong refugees had been given the right to vote in the state.
In the end the party did however decide to contest, this time allied with Indian National Congress.
The leadership of the party is called Arunachal Congress Working Committee (ACWC).