With a little more explanations: What is in the plugs in the plug folder just adds to what is inside the data files (the ones in the Nova data folder), the data files (containing the whole Nova scenario) are still there. Now, resources with IDs in plugs replace the ones, if there is one, same ID-numbered resource in the data files, but everything else is left untouched; especially, some systems in the data files say they link to some system ID you replaced, making it link with the replacing system. Think as plugs as an easier and lighter way to distribute little modifications, avoiding to have to replace the whole data file (as was needed with Maelstrom sounds/sprites/whatever, even if only a few were altered), patching the already available data files. Now if you do not want to be based off the Nova scenario, use and distribute your plug as data files needing to be put in the Nova data folder instead of the plug folder. Notice, though, that it will make you require to put your own ships, govts, outfits, and the like, not just systems.
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