Awesome game! Yeah it doesn't really fit the theme, but I don't think that matters too much since the game you made was fun.
The stage with invisibility could definitely be clarified more. From what I can tell, you lose when you run out of bullets. But when you introduce the stage with the invisibility, you only give the player one bullet, which leads them to believe that shooting enemies from stealth causes them to lose. This confused me for a while, until I looked down and saw that there was only one bullet in my inventory. Also I couldn't figure out that level, since the bullets don't seem to pierce enemies, and you can only kill one enemy with the door and another with a bullet.
Overall pretty sick game, I had a fun time with it! The level design was awesome, really made me feel like a badass spy
Edit: I noticed the solution to the level in the comments, and yeah it definitely needs to be explained more. The tutorial specifically says right click to kick down doors, not any object. Also the levels always end whenever all the enemies die so I didn't expect the intended solution to be what it was at all