Each mission has a ranking as follows.
Ninja - Don't get spotted.
Ronin - Take out all baddies in the mission.
Roninja - Don't get spotted, and take out all baddies in the mission.
The terminals that are marked on your map with a blue diamond. Some require RP to unlock so keep playing to unlock them.
As for the game itself, it's hard and unforgiving. One hit deaths will mean you respawn from last save point. Practice will be required.
The missions can be found below. To check which one you have done, pause the game and move your stick right to View List.
Par for the Course
The Wing Man
The Naked Blade
These are the only missions that have shown up for me, so I'm presuming that this is a complete list. If it changes I will update. Good luck.
Ninja has 20 missions attached to it.
Ronin has 22 missions attached to it
Roninja has 20 missions attached to it.