Interesting premise and I actually found that I enjoyed the light stealth mechanics quite a bit. That's not usually my thing, but it felt really good here. The movement also felt fast and responsive on keyboard.
While the player jumping to the back of enemies during the backstab attack is a great touch, it would help a lot if there was some additional animation from the player character. It took me a few tries to figure out when the backstab was working and even then there were times when I died because an enemy turned around on me while I thought I was backstabbing.
There also appears to be an issue where the player can fall out of the map if they turn around immediately after loading into a new room. I think the player character scene is being placed inside of the Area2D colliders that are used to detect when they exit a room when they should be just outside the collision shape instead. Thankfully, your save system means this really is not all that much of a setback for now.
Overall, this was pretty ambitious! And managing a large team can take a lot of effort. I also like the story elements that were in there. Great job!