Ships on autopilot do not stop when sensing enemy ships.
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Stardock Forums
Some time ago code was put in to have a ship drop out of autopilot when sensing an enemy ship. I had a Battle Cruiser that was badly damaged that I put on autopilot to get to one of my stars that crossed the path of the Torians (they declared war on me many turns ago) and distroyed the Torian ship and then dropped out of autopilot.
Sorry, I goofed and don't have a saved game.
Sorry, I goofed and don't have a saved game.