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If you are using mods that allow you to just fly nonstop, you can't just fly to the end of the stage and into the return home portal. This doesn't work for some reason. It seems there are certain things in the level it keys off of in order to complete the achievement. I finally just ran through doing as little as possible because you will more than likely kill a rat accidently when trying to hit a barrel into an enemy as you would actually needing one. I think the duct spiral towards the end may be the key. You may try flying all the way to the end and going up the spiral and then through the portal.