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About the story : Come on Wube, don't you want to have a legion of teenage girls writing Factorio fanfics ?
![Laughing :lol:](./images/smilies/icon_lol.gif)
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There's one thing that Factorio can do in mission transitions (for better or worse), that most RTS can't : blueprinting your whole base, picking it up, and then putting it down again ! (I should try again that game with super-low resources where you have to keep relocating...)
You could, in the manner of Homeworld's "quick auto-collect all map's resources once the mission is won", have Compilatron do it for you with a click of a button, and serve as a big "box on wheels" ?