This is story related and cannot be missed unless you experience a glitch. It is unlocked upon completing the 9S Captured main story quest. There is the possibility of a glitch. So, make a save at the City Ruins: Deep Cave access point before proceeding in the direction of the story mission objective marker.
If you get the Olive Branch main story quest without unlocking this achievement, you have experienced a glitch. If this happens, clear the cache. To do so, turn off the console by holding the
on the console for at least ten seconds and then unplug the console for at least 20 seconds. Load the save you made at the City Ruins: Deep Cave before proceeding to the Copied City. Clearing the cache will most likely remedy the problem and you should earn the achievement when you complete the 9S Captured Mission.
Spoilers:
*** Spoiler - click to reveal ***After completing the Redheads main story mission where you acquire the scanner, press the menu button and tab to Skills. Select Pod Programs. Assign the A170: Scanner program to one of your pods.. Refer to the following guide if you need more info on acquiring and using the A170: Scanner:
Solution for Harvest King In NieR: Automata BECOME AS GODS Edition
Fast travel to the Flooded City. Switch to the pod to which you have assigned the scanner program and press the left bumper (assuming you are using the default controller configuration). The scanner will beep more frequently as you get close to a hidden item. It will reveal items and YoRHa units with very faint life signals.
Go slowly pressing left bumper continuously so you will discover all YoRHa units with faint signs of life. As an added bonus, you will find a weapon, the Iron Will, in a depression just off the right edge of the surface you are on. There is a YoRHa unit nearby so make sure you identify both hidden items.
Towards the end of this section, you will spot a YoRHa unit near a bus. The YoRHa unit gives you coordinates you can use to track 9S.
Fast travel to City Ruins: Deep Cave. Make a save. Follow the objective marker. There is a branch in the path but you will be able to see which leads towards the objective marker. If you take the wrong branch, your pod will bring this to your attention. Following the objective marker will take you to the Copied City and a multi-phase fight with Adam. When you complete the final phase of the fight and rescue 9S, the achievement unlocks.