Dawntrail is the first expansion where I started skipping cutscenes. The story is bad

[Karkarov]

I never skipped a cutscene.... but by the final zone I was definitely checked out, not emotionally invested, and just wanted it to end sooner rather than later.

That said in the only defense I will give this story, your read on the final zone is wrong.

You don't genocide anyone, all of them are already dead, you are talking to computer driven AI facsimile simulation of people based on their stored data memories. They, like the zone they live in, are not real.

You shut down the nodes to make her vulnerable for a moment when she catches they are shut down, that works. You "hope" she will just stop when she realizes it is pointless and the endless have been deleted.

PROBLEM: Sphene is also just a AI simulation that has been hard coded to do anything to keep the endless simulation running. She has no choice, she is just a program doing what it was programmed to do. That is why she doesn't stop even when continuing will serve no point.