Does the game even have an ending? It is already the year 2000, and for about half a year there is nothing new, no research and progress. Just fighting off UFOs and doing rescue missions...
Yes, there are a couple of cutscenes for finishing storylines and the final vanilla ending of Cydonia which ends the game. In this mod reaching Cydonia still requires Cydonia or Bust and the Avenger but there are extra steps to research Cydonia or Bust, without spoilers focus on space travel technology and capture Ethereals (should be appearing now in 2000) to unlock the final series of missions. Waiting on the Ethereals to appear was the most tedious part for me as I had to wait until around 2000s myself too before I could get one.
For more spoiler filled direction
You need to beat the orbital space station to autopsy the brain and research an ethereal (you can't research a keeper from the station before researching another one or researching reptoid from final zombie mission) this on top of other research should allow you to create a satellite facility and launch a manufactured satellite into orbit. Once you have the satellite in orbit you should unlock the moon missions once a month like HQ missions. Finishing the final moon mission and capturing the Ethereal Grand Master (white robe with red tabard) from the final moon mission. This should give access to Cydonia.