Episode

MissionStart

This section is for setting up the solar system map, what objects are visible during the briefing. 'Parenting' objects to the mission area (not exactly sure on the purpose of this) and enabling/disabling commands or handling the resource management aspects of the game.

MissionEnter

Looking through the original files it appears that here you do the final bit of tweaking and tidying up immediately before the mission launch and of course, issue the actual command to launch the mission.