There is a big hall at the start of mission, full of humanoid robots and 4 turrets, protecting the entrance to the Calculator's room. The big red robot surprisingly turns out to be a cyborg (humanoid Brain Bot), based on General Barnaky brain and eyes. If you have General's locket or Barnaky's letter, he eventually retires from battlefield, due to inconsistency in his behavior, he discovers. You will meet him (not hostile) again, near to Calculator itself, thinking about his life.
When your squad reaches the Calculator's room, the Calculator will raise indestructible barriers around itself. You will need to destroy the brains near it to access the first door near the Calculator (before destroying the brains, read solutions 1 and 2). Behind it you will find some robots and another brain. If you destroy that brain the second door opens. There are three such doors, each containing a brain. If all the brains are destroyed, the barriers lower, allowing you to access the Calculator and listen to its offer. There are four ways to end this mission, each resulting a different ending cinematic.
Sacrifice your character to fix the Calculator with good karma. Since destroying the brains in the calculator's room gives you a lot of negative karma, you need to place explosives near the brains so you are not attacking them directly (This presumes you already had good karma at the beginning of this mission).
Sacrifice your character to fix the Calculator with negative karma. Destroy the brains by just shooting them; each will give you negative karma and of course will open the necessary doors.
Do nothing and wait or destroy the calculator by attacking it. Brains can be destroyed any way you like (the Calculator can be destroyed without alerting it; it can be shot from outside the room avoiding the three rooms with brains).
Accept General Barnaky's offer of sacrificing himself. This only requires you to talk to him after the Calculator has made the offer.