The Atlantis Project was a throw-away mention in the Morrow Project module, "Prime Base" with an implication that it was to be activated 150 years after the fall of civilization.  The reasoning was (apparently) that it would take that long to rebuild the US and allow it to assist the rest of the planet.

 

My version of the Atlantis Project has a different approach and (like the US version) is intended to start operating in the 3-5 year period - but planned for the possibility of having to wait for up to 75 years.  Therefore there is no overlap with the "canon" game, which is set 150 years after the collapse.  The Morrow Project might find traces of the Atlantis Project (or be contacted by descendants of the original personnel).