Mm, maybe if you create a variable in mission template for castle assaults (ladder and belfry) that active second menu when player do something in "native" part.
By example:
-Normal assault menu. Player choose play it.
-Load normal scene, and when player get walls, you assign a variable 'walls_ok'.
-When that part of the battle finish, if walls_ok is active, new menu should be open with new phase for assault (streets) - (where you can load your new scene and new mission template).
-If walls_ok no active, then it load native menu for other assault. Or if enemy havent more troops finish assault.
This can take long to do, but it shouldnt be too difficult...