Perfect Dark on Nintendo 64 - Special Agent Mission 9 : Skedar - part 1 : Skedar Ruins: Battle Shrine
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1. Identify temple targets
2. Activate bridge
3. Gain access to inner Sanctum
4. Assassinate Skedar Leader

1. Identify temple targets

To start the mission off right, go to the pause menu to activate the "R-Tracker" directly. This displays the radar in the top right, letting you see where the 3 pillars you need to blow up are located. There are 5 pillars in this first part of the level, so it's important to recognize the right pillars, since you only have 3 "Target Amps" and can't afford any mistakes. If a Target Amp misses its target, you'll have to start over, so be careful to kill the Skedars nearby so you don't get thrown off by a bullet or a hit while launching the Amp at a pylon. I won't draw a map since this first part is quite small. The 1st pylon is in the "room" right after the start. Then follow the corridor (watch out for invisible Skedars along the way). At the end of the corridor on the right, there's a second pylon behind a wall you can go around (careful, a Skedar is watching it). At the end of the corridor on the left, there's an intersection. Straight ahead is the rest of the level, remember the spot, we'll come back for Objective 2. To the right, there's another corridor with an armed Skedar at the end, which I recommend shooting from a distance. Just behind him is a second pylon. At the end of the corridor to the right (and just before), there's a "door" on the right leading to a "room" with 2 new Skedars armed with a Reaper. Kill them and cross the room after picking up their weapon. The fourth pylon, much bigger than the others, is on your right, at the top of a staircase. To reach the fifth pylon, you need to go around the wall to reach one last "room" with 2 new invisible Skedars. For each pylon you need to mark, take out the Target Amp and launch it at the pylon. Once the 3 locations are amped, you can continue to the rest of the level by backtracking and taking the right at the end of the corridor. Be careful not to pass too close to the marked pylons, since the Maians are going to blow them up.

2. Activate bridge

At the end of the corridor on the right there's a small ladder. Before taking it, shoot the Skedar facing you. If you zoom in with your Falcon, you should see that the ladder slightly to the right of this enemy is blocked by a wall, whereas it wasn't in agent. Take out your Devastator in wall-mount mode and aim at the chunk of stone blocking the ladder to blow it up and free the ladder. Before going down, crouch and approach the ladder to find the right angle to kill the Skedar waiting for you down and to the right. Once the threat is eliminated, you can stand up and jump over the chasm to reach the ledge across the way. In agent, you can also jump onto the ledge across the way and kill him from there. Once you've made the jump, take the ladder freed by the Devastator and keep going straight until you reach the wall, after a drop down and a short corridor. Turn around to kill the invisible Skedar that reappears to hit you, then turn to the right with your scanner to notice that the wall is weak. Hit it with the Devastator (in "wall-mount" mode) to create an opening and enter the building, where the doors struggle to open — you'll often need to press several times (as soon as the opening stops). Follow the corridors, killing the mini Skedars, which are more numerous than in agent, with your Falcon 2. Once you're sure there are none left, open the door on the right and eliminate the last small Skedar waiting for you in the room.
Note: the small Skedars seem fast and hard to target, but in fact they all have the same behavior: they stop at jumping distance from you, wait a moment, then jump at you. I recommend backing off a bit when they freeze; they'll then land a little in front of you, and you can kill them on landing, since they also freeze slightly at that moment. You can also target them fairly easily before their jump, but it's often safer to keep the required distance in case you miss them.
Push the block with the logo on the beige background so it goes a bit further than the post, then shift to the right to push it left onto the beige slab with the same logo as the block. A bridge then appears.

3. Gain access to inner Sanctum

Exit the room and go right to take the bridge that now lets you cross the chasm. The scanner can be handy for spotting the small Skedars more easily in this environment, where the lighting is no more stable than the doors' opening mechanism (looks like an electrical problem). Follow the corridor to a fork. This time, before going up on the right, take the door on the left. You'll run into a first Skedar shooting at you with the Slayer (rocket launcher). The rocket isn't super fast, so once he's fired, take a few steps sideways and kill him. Watch out, he reloads fairly quickly, so you'll probably need to dodge a second rocket. A second Skedar is right on the right and also has a rocket launcher, so use the same tactic (or, like me, you can use the Slayer in guided mode to kill him safely). Once at the end of the room, you can for example kill the Skedar on the bridge with the Slayer's last round and leave the Slayer as an offering (you need to equip it and press B in front of the altar). This activates the generator; turn back, go back up through the room, take the door then the small climb across from it. Cross the bridge calmly if you've killed the Skedars below, open the doors (and complete the objective) and you're now in the famous Skedar army room. In special agent, this fight is optional and quite dangerous. That said, having a Mauler with its ammo for the boss is really great, so it can be worth killing them without spending too much ammo. The Reaper in chopper mode isn't bad, but you risk taking damage. In spray mode, it's not much better since it sprays so much and also wastes bullets, but combining the two, possibly waiting for them in the cells, you should get through it. Once the army is wiped out (or not), take the door opposite the one that brought you into this room and follow the path to the boss.

4. Assassinate Skedar Leader

This fight is a bit unusual since the queen is on a platform and can't be killed directly by shooting her. In fact, you'll need to deplete her shield enough that she goes to recharge at the central totem. During this, the totem is only partially protected, and you'll need to break the unshielded pieces (for example with a charged Mauler shot). Between shield-destruction phases, the cult leader can teleport near you, and you'll need to move to avoid him. He can also send a skedar onto the battlefield; I recommend eliminating it quickly since it can hurt a lot, and in any case it will get in your way of aiming properly at the totem. Finally, he can also shoot you with the Slayer. Generally, he aims at you, so if you move perpendicular to the shot, you should be able to avoid it without too much trouble. At the start of the fight, wait for him to start moving before shooting at him.

Mission End

The end of the mission is also the end of the adventure. The totem impales the Skedar king and, after one last challenge, Joanna and Elvis manage to escape the planet (even though it isn't shown) and the Maians will violently bombard the planet. Peace will thus return to the galaxy. While the main adventure is over, there are still 4 special missions (bonus levels) remaining, starting with Mr. Blonde's Revenge.

After the level's ending sequence, and despite the remaining bonus levels, the credits sequence triggers. Go watch it.