I'd guess you'd need an addon with the alternate end dialog in it. You could put an onLoad handler in this new version, to call your script in order to update it with whatever you want to change in it. Problem is that all missions would see this new dialog if the addon was installed. You could make any extra controls invisible at the start and only show them if your script was called (in your mission, that is). Frankly, though, I'd be afraid of potentially messing up every other mission...