Before exploring the bunker under the Citadel, the Shadow Carja stronghold, you have to find a way to disable the Eclipse focus network first. Following Sylens’ instructions, you need to travel to the marked point to the far west, deep in the jungles. Find the escarpment where you need to climb on. This is placed near the crevace that’s oozing up fresh stream water. Use the climbing holds to reach the campsite in the alcove on the face of the cliff. Use the campfire to trigger a cutscene and start the next part of the quest.
After the scene, enter the tunnel to reach the isolated part of the woods with corrupted machines roaming around. They can’t attack you while you’re inside the tunnel so use that to snipe a few machines off. You don’t need to kill them all but if you want, there’s a lot of tall grass that you can use for cover. Follow the objective marker then look for climbing holds on the rock wall. Use that to reach the ledge that will give you access to the next area.
Next, you have to deal with corrupted scrappers. You can snipe them from the ledge or simply deal with them head-on. After clearing the area, follow the marker and continue climbing up the obstacles until you reach the ridge. As Sylens suggested, the rappel point in the middle of the bridge will be your escape point later on so take note of its location.
For this next part, you have to take out the cultists patrolling the area. You can go loud if you want or deliver stealthy kills. Make your way across the bridge while clearing the path of threats. When you reach the hut, you can examine the scattered data pads, Helis’ armor, and the mural hanging on the wall. When you’re ready, push the old rotten trunk to create a bridge for you to cross.
Follow the valley path until you see the derelict tallneck ahead. Use the wooden scaffolding to reach the top of its head. Upon reaching the top, a cutscene will play.
After the scene, you have to literally run for your life. Keep running and time your jumps carefully to be able to grab hold of the climbing holds and keep moving until you reach the relative safety of the upper grassy cliff. This time, you’ll have to deal with a lot of eclipse troops. Ignore them and keep running. Heal as necessary and follow the objective marker until you see the bridge. Run to the rappel point, press the prompt to rappel and watch the following cutscene. Mission complete.