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I have conquered enemy base but I can't keep it. Can I remove it out of the map somehow?
only way I know is the destroy base command
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Kuokkanen: I have conquered enemy base but I can't keep it. Can I remove it out of the map somehow?
Right Click on a unit that's inside the city -> Action -> Obliterate. Has to be a military unit I think though.
As the others have stated, you can use a military unit to destroy the base, but remember it is an atrocity and will have negative consequences.

http://alphacentauri2.info/wiki/Atrocities