hey! I really like games like this where you have many upgrade paths :)
Some suggestions for improvement:
I would recommend you to add a webgl export, so that more people try out your game. People are always hesitant to download a build.
I also would recommend you to speed up the gameplay loop. I spend 3 minutes running around scanning boxes and didn't find any encounters. Reduce mission time and increase ghost encounters and the game would feel way more engaging.
nice submission! :)