Go to the Interrogation Room. Get the Class A Security pass. Go to the temple and get the book, then open the chest to get the sacred axe. Use the sacred axe with the OmniBrain. Major Benson arrives. If you do nothing you will be killed. You can either action Major Benson - he'll be killed and the glass around the OmniBrain will be smashed, action the OmniBrain, in which case you will smash the OmniBrain and then kill Benson, or duck down behind the OmniBrain, in which case Benson shoots the OmniBrain and dies. Providing you've survived, you can then go down into the Founders room.
Have a nice long chat with the Founder, then Action the computer. You have finished.