I've done something like that before. I used the call command for that. The whole game I made was 23 Batch files
Sounds quite simple, make a main menu like Jacob's first post and call a random mission batch on selecting "mission"
Though including those external batches in labels might be handier. Even then you could add labels with call commands later after the labels with batches... if you get what I mean.
Kinda modular system..