I have two games.

The first one I found out was called Nanosaur and even has a free download. I played like 20 minutes of this in grade school one day and never got a chance to play it again during my childhood.

The other is insanely obscure, because I'm pretty sure I know the name of it but cannot find any trace of it. It's a fantasy themed RPG maker XP game I'm fairly certain is called "The Under" Where it starts as a training mission but your team discovers strange things going on and reality re-writing itself. It uses a real-time turn based combat (similar to final fantasy) and...

spoiler

Everyone in the party except the kobold dies at the very end.

I'm also fairly certain the person making it started working on a sequel that had a small demo I played. A quick google search brought up another RPG maker game called The Under, but this isn't the game I'm talking about.