The main character is a militar from any country. The leaders of your country tell you that you have to go to a country to protect it from rebels, and you go thinking that you are being praised for being compassionate and kind because someone says so; but then when you are going to fight in the capital you discover you were fighting the government and you then realise you were being evil the whole time.
If you want anymore ideas, please say so

what kind of game are we talking about here
like a 2D top down or like a Prison Architect/RimWorld?

More of a 2D top down

But what about character development? Is the main character someone who just takes orders without question or does he have speculation but does what he is told, or other options.) These are just basic questions of course. Put yourself in the main characters position and then present that. I'm all about video game ideas, but they need to be plausible at the same time. (Just trying to help/curious please don't hurt me)

The main character will be able to choose what to do in some missions, but in many he will just be commanded to kill. I was thinking that he could be a good guy made to become a serial killer for his army.
Also, he could do some good things for the people that he purposedly "saved" to gain positive karma; the Karma will be a measure level of how benevolent you can be but it will get worse after each mission but if you help people in between missions you are able to get some positive points which at the end of the game is explained and if you have a lot of negative points the last mission will be incredibly harder than if you did all the good things