It sounds to me like you've got a basically hierarchical set of containers and items within those containers (items can be containers themselves). For example: a world, bases in that world, items in those bases, people in those bases, etc.
Rather than a database I'd suggest using an XML document as your 'development' save file. I've found this to be useful for two reasons:
1) Its human readable and easily tweakable by hand to test different scenarious.
2) Its a cinch to convert/write alongside a persistence system that writes to an XML file to a persistence system that writes to a custom binary file and just change the mechanism used based on debug or release modes.