A friend and I experienced slow-mode while playing. We discovered the F4 debug menu and under "Update" it lists "mod-EndgameCombat" with a high update value (20+). It would seem that alien tissue drops create a performance hit increasing in severity as the drop count increased (10,000+ drops). The fix was of course to run around collecting as many alien tissue drops as possible (Thank you deconstruct planner with whitelist 'item on ground'). We disabled the 'auto deconstruct' mod option to prevent construction bot massacres during relentless hard-mode alien attacks.