Storyline Dilemma

I've been thinking today of the overarching narrative that I'll include in this map.
In my film class at university, we started analyzing Inception. The story in it holds a lot of similarities to the one forming in my mind, so I was thinking the entire time how I'd be able to use the same concepts.

The biggest decision I need to make in this map project is the finale of the story. I know that I want to include a moral dilemma and I have something of an idea right now, but it's not fleshed out at all. In essence (and this is what I was building as we watched Inception), I need the player to choose between two world-changing possibilities, both of which will affect the future. It *must* be their choice and I need them to be invested enough emotionally that they truly feel torn, the feeling that true dilemmas bring. It has to be so powerful that they should have trouble when it comes to the decision moment. I don't want to lead them along a single path which they completely resolves when it finishes; this choice should feel important to their life outside of the map experience and I'd love to see further discussion brought about solely by this dilemma.
That's how high I'm setting my sights for this story.

In the video series on my YouTube channel, I plan on taking some time to figure this out as I build soon.

Supplemental:
I believe I want the creature to have discovered something that will imminently eradicate life on the player's planet. With the player building the machine, they are creating a way for the human race to ascend into energy and either be transported to another habitable planet or move into the creature's dimension to live. That choice is contrasted with the opportunity to remain on the planet and battle through whatever the danger is and with only a tiny chance of survival. What the creature is proposing is a decision of whether you want to run or you want to fight. I'd bet that, with this initial choice, most players will want to stay and fight. However, I need to make sure they understand the problem and both solutions very well. Maybe I should expose the problem with around three dreams left, so they still have time to gather a few artifacts while they think.

So why would anyone choose to leave? How can that be a better choice in some instances? Would there be some cons with the travel or destination? I want the choice to run to be a valid one. I'm pretty sure my ultimate goal is to see the player squirm, really struggle, when they reach the point of decision. Not because I want to see them in pain, but because it would be a victory to capture the essence of tough choices that have big consequences. Maybe I can vent as I build.