Requirements for completing Star Trek Armada Dark Omens mission?

Solution 1:

Running on Windows 10 platform. I replayed the mission. I flew my extra ships (ships that I built for the mission) to the shipyards and decommissioned them to reclaim the resources. Then I left the Enterprise in range of the very last Borg target: their dilithium collector. When I had the Enterprise destroy the ship, then the cutscene came on and the mission was finished.

Link to animated gif showing the process: https://gifyu.com/image/GLiD

I don't recommend using the cheat to skip the mission since it creates substantial glitches in the game: too many to count.