i am having this same issue. i'm running DA 1.6. i defeated the dread lords entirely and went through maybe 100 turns after, no mission ending. Victory screen in the shows 100 percent victory, but still no actual victory.
the only thing i could think of is that i was destroying colonies after overtaking Dread Lords planets, due to the instability of my economy. after reading this thread i went back and used cheats to check the map, all the Ctrl+U cheat did was add Rally points all over the map and not reveal anything. starting the mission over and using cheats to win quickly (various different ways), there was still never an endgame after defeating the Dread Lords. i also tried 1.6a test build and still the same problems.
i also have had some other issues with AI throughout the entire campagin, playing the Dread Lords campaign using the Dark Avatar expansion, especially in comparison to having played most of the campaign before (up until apocalypse) with the original DL game. the biggest issue i've seen is that the AI have been colonizing absolutely or almost nothing in the missions. this is with difficulty on 'tough' and i've tried "force ai to use max CPU" both on and off. this seems to be mostly only a problem with the team races. they literally colonize nothing and contribute absolutely nothing to the missions. they build a troop transport and a defender and that's pretty much it... leaving them right at their home plane the whole time. once something comes and kills those ships, they rebuild them. they never even attack the Yor or Drengin at all it seems. also, since the team members are doing absolutely nothing, letting my civilization become incredibly powerful in comparison, they insist on eventually plastering me with agents. i know they're not all coming from just the Yor and the Drengin. it seems kind of odd for "Team" members to be crippling my planets and not even touching "enemy" planets. this honestly gets to the point of me having absolutely no spaces without agents on them.
i went back and opened up the DL chapter and started to play Apocalypse that way and the comparisons were like night and day. every planet was claimed in the first few months and every problem i'm having using DA for this campaign is entirely gone. even using cheats to win Apocalypse on the first turn (reaveling all, then making the DL surrender to me) brought me to a victory after hitting the turn button. even that is not working using DA.
i mean i guess i could just deal with it and play the DL campaing using DL chapter of the game. but i'm pretty sure it's meant to be playable correctly using DA.
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