- This level occupies the map slot MAP09. For other maps which occupy this slot, see Category:MAP09.
Fifth mission: Kill the Programmer
Enter the door in front of you. You may optionally go into the room straight ahead into the large room, and click the image of the Programmer; this unleashes a Sentinel ambush, but after they are all dead the bars reopen, and in the northern alcove where some of them were is an Ammo Satchel (and in both alcoves are medical kits). But if you already have an Ammo Satchel, it's probably not worth doing this room.
Go around either corridor into the next room. From now until the end of the level, be prepared to shoot your way through. At the end of this particular fight, if you need supplies, the north gallery (left as you came in) contains four ammo clips (in addition to the clips dropped by the Acolytes) and a med kit; the south gallery contains a med kit. Then press the switch on the back of the altar to lower the stairs to the rest of the level. Probably the best way to take out the Acolytes waiting for you at the bottom is to lob a pair of Phosphorus Grenades down there.
If you need them, in the room to your left as you pass through are two med patches on the floor, and a surgery kit and box of rockets in a hidden room (A) at the top of the other staircase. To return, either go back up the original staircase (it has a gap, so watch out) or (probably easier) lower the column in the middle and ride up on that, then jump across. In the room to your right are three rockets.
Go into the huge next room and up either staircase; beware of a Crusader coming up behind you (and the one on the other side). After you defeat them, in the niches where they were are (on the two easy difficulties): in the north one (B), some HE Grenades; in the south one (C), a box of rockets. (On the other three difficulties, both contain two Energy Pods each.)
When passing into the next area, be sure to go around the block in the middle (D); if you take either of the other routes, a gate to a teleport landing pad will open, allowing Acolytes to teleport in. (There are two med patches in each of these areas, and three Energy Pods in the northern one, but they're probably not worth the risk.) If you double-back and enter (D), you will find some HE grenades, a box of rockets, three bullet clips, and two med patches. But watch out for the Acolytes in here, including a Shadow Acolyte.
Continue through either of the middle passages (going through either of the others will trigger the trap described above); watch out for the third Crusader (and the fourth, if playing on one of the two hardest difficulties). Continue up the central stairs (there are two med patches at the bottom) into the final area, which has a huge structure with a flight of stairs leading up to it, and the Programmer sitting atop the stairs in a flying life-support pod (unless he has already awoken before you get here). Shoot the Programmer using missiles, all the while dodging his lightning bolts and the spikes on his pod. When he dies, you will black out and reawaken in front of Macil in the New Front Base; you will also find yourself in possession of the first Sigil piece.
- At the southeastern end of the area atop the pyramid, press on the protruding wall to reveal a secret area (unofficial in the original, official in the Veteran Edition). This contains Metal Armor, a box of ammo, two Medical Kits and (on the three highest difficulties) a Surgery Kit. In the Veteran Edition, this is a secret which counts towards the Completionist achievement. Note that since you need to get past the Programmer to get here, which is a difficult and dangerous task, it's probably not worth doing unless you need to do it for the Completionist achievement.