Alright, people, listen. I don't think anyone's talked about the one three-act game that I can think of--Homeworld!
Think about it. The first bunch of missions are you fleeing the Taiidan's overwhelming forces. But even as you're doing that, you're very slowly and painstakingly building frigates and bomber wings (or Defender screens). Throughout this, your main goal is to get to your homeworld, while not dying. In fact, plenty of 'win' conditions are actually "escape the battlefield with as many intact ships as possible". It's a survival RTS.
Then, as soon as you have a balanced (albeit small) fleet, Act II begins, and you're taking out Taiidan outposts like the Supernova Station or entering the derelict graveyard. This is the stealth part of the game--it's not really stealth, but the enemy AI won't trigger until it sees you, and taking it head on is suicide. The Supernova Station is particularly good at this--there are plenty of paths, but you absolutely have to find the weak point and you absolutely should keep your forces hidden until you're in a strategically advantageous position. Again, you have a fleet, but if that Taiidan fleet came right at you, you're dead.
But then, several missions and a lot of salvage corvettes later, you have a large fleet. This starts with that level where there is a sphere of around 250 ion frigates for you to destroy/steal, and all levels after that. This is Act III. I've had trouble explaining to people who haven't played the game why Homeworld is so satisfying, and now I know why. It's definitely because it adheres to this tight, well-proven plot structure. It doesn't give you the tools to fight an obnoxious enemy until the last third, but when it does, you know exactly what to do. And the fights have more purpose than any other RTS I've played--those Taiidan have been after me the whole game, but now finally I have a chance to throw a punch (and then some).
Since I first played it back in the day, I've felt that Homeworld told the best story of any video game, and I think now I know why.