Mission where you (or an ally) *should* die?
You can actually. Set an ally to betray on the completion of an optional objective, such as a blinky. Unfortunately you can't set the betraying ally's defeat to be required for mission complete.
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You can make it so that the most "desirable" result storyline-wise is to actually fail a mish--be it by running out of time, letting someone get away or an ally die etc. I'm not sure, but it may be possible to set an ally's survival as required to complete a mish, but then also set him to betray you after the completion of a certain objective.
That said I'm not really sure what you're trying to get at, though I'd steer well clear of anything that has heavy-handed and player character within the same sentence.
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The vague thought, which may not work, is an arc where you are defeating your arch-nemesis, and you end up going back in time to try to find out what went wrong, and it turns out that what went wrong is that, long ago, you beat him up for no good reason in school, or the equivalent, and that if you could just prevent that from happening, no cities would have to be overrun by unstoppable robot armies just so he could try to get back at you.
I'm not sure it's viable, I just sorta liked the notion.
I had a vague notion of doing an arc where the win condition involves being defeated, but I assume that's impossible. But wait! What if we used time travel, and you needed to cause your Younger Self to be defeated? But not to defeat him -- to let or help someone else do so.
I've realized there's a fundamental limitation, which is that so far as I can tell, you can't have an NPC who is either an ally or an enemy, but the player decides which.
Hmm. Thinking about it more, maybe I should just be heavy-handed and declare by fiat that you are helping to defeat your younger self.