It would be interesting to use the SM to make a huge "generational" ship with high tech stuff and cargo holds full of enough engineering teams and minerals and such to set up a colony and start building things as well as some bonus cargo holds with high tech ship components (military stuff, since making the big ship military wouldn't be feasible due to maintenance problems). It would be jump capable, but badly damaged. Then you make a second empire with low tech and gift the ship to them, getting rid of the initial empire. You could include a few small scout ships with which to fly ahead and scan things while the big one slowly moved along. Using the other empire you would load it with colonists and whatever before moving it into position and nuking the starting sector.
The story could be that you are a fleet sent off from some distant place to escape from some big disaster or enemy - something went wrong along the way and it took way longer than you expected, so it turned into a generational ship and you lose all knowledge of your old technology by the time you get there. You still have parts left from scrapping ships along the way that stopped functioning, but actual tech levels are minimal.
You'd start the game in an empty sector with a couple jump points mapped, so the actual gameplay after the start would be totally random. One game you might luck onto a rich system and plant roots immediately, another you might wander for years seeking a good place to live. After you did set up a colony you could either use the ship parts in the hold to build some good ships, or take them apart and try to get all the tech you could from it to build more later. The same thing with the ship itself - take it apart for the technology, or try to patch it up and keep using it.
It would take some setup, but it would be a fun scenario