I've done something like that before. I used the call command for that. The whole game I made was 23 Batch files ![Tongue :P](https://www.computerhope.com/forum/Smileys/classic/tongue.gif)
Sounds quite simple, make a main menu like Jacob's first post and call a random mission batch on selecting "mission"
![Tongue :P](https://www.computerhope.com/forum/Smileys/classic/tongue.gif)
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..