That sounds fun, and something that'd actually translate nicely to the RPG Maker template. It's also something that takes skill to pull off well, you'll need to play with how the player will initially frame the stuff you show to be going on, and how the stuff should actually be interpreted. Not coming off as heavy-handed is going to be tricky. Also, pulling this off is based on knowing how to use the medium, so if this is the first RPG Maker thing you're going to be doing, it's going to be particularly challenging.

There might also be a disconnect between games and movies here. Movies tend to always go out of their way to portray the protagonist's side as good, while games have a lot more of just semi-symmetric opposing factions. You get to play as the kill-happy Zerg or Undead Horde, and nobody pretends you're siding with the noble savages against the inhuman oppressors. So the players might just go, "ooh, I'm the Zerg, cool!" or "I guess I'm supposed to defect from Zerg to Terran here".

Random other thoughts, Battlezone 2 has a similar plot twist with off-script player action needed, though both factions are high-tech. Dominions 4 has Asphodel that's a neat corrupted nature spirit faction. Though I'm guess you're going for nature just being inherent bastards instead of the more common corrupted nature striking back trope.

Also, games really train people to stay on the script nowadays. Games that let you go rogue with an actual in-game-world action instead of choosing 'yes' on the blinking "DEFECT TO TERRAN SIDE" dialog are rare, since letting the player go off the script in-game and meaningfully interpreting their actions is really hard in the general case, and really frustrating for the player if they have to guess the particular special case where the off-script action actually opens a different plot branch instead of just leading nowhere like it did in the 10 previous levels. The original Deus Ex did have bits where you could mitigate the shit your early game actually evil employers were pulling with quick in-game thinking, but going over to the rebels was still always in the script.

So, overall, challenging project. You need to figure out RPG Maker and where to get the art assets and such, if you're not already skilled with it, you need to do worldbuilding for two worlds, and neither can be a cardboard cutout for the conceit to work, and you need to figure out how to make the game narration work so that the player can both get effectively tricked and has all the necessary pieces to put together the alternative choice during play.