Nier: Automata offers a variety of sidequests over multiple story routes, but not all of the quests are clear-cut when it comes to completing them. The "Retrieve the Confidential Intel" quest is one of these, as players often find themselves unaware of how exactly to finish it.
Fortunately for you, we've got a full quest walkthrough right here, so you can complete the quest and earn your rewards without any further confusion. Here is everything you need to know about where to accept the "Retrieve the Confidential Intel" quest and how to get the proper ending to close it in your quest log.
Retrieve the Confidential Intel Walkthrough
This sidequest becomes available after you have completed the main quest "Assault". You can accept it by speaking to the Resistance Member found in a building in the City Ruins. He can be found near to the access point in this area and also close to where Engels is, as shown above.
This guy will ask you to collect three Plug-in Chips, all of which will be marked on your map. Head to each location and battle with the machines there to retrieve each chip. After collecting your second chip, your Pod will comment that the chips you are collecting are YoRHa unit chips and that Resistance members should have no need for them.
Once you have all three chips, you will receive a message from Command that there is a missing YoRHa unit that had classified information and that it must be found immediately. When you return to the Resistance Member, you can decide whether to give him the chips or not. Refusing to give him the chips more than once will prompt 2B to ask him if he knows anything about the missing YoRHa unit, but he will say that he does not.
Many players find themselves stalling at this point, as they don't want to hand the chips over. However, in order to progress the quest, you have to hand the chips over whether you like it or not. You will receive the quest rewards at this point, yet noticeably — the quest remains uncompleted in your quest log.
The rewards obtained are: Skill Salve (L) x1, Crushed Nut x3, Dented Plate x4, Large G Luck x1, Large Recovery x1, 5,000G, 600 Experience Points, and the Pod Program: A140: Gravity.
Go to the Desert Zone Housing area and you will be able to find the same Resistance Member in one of the buildings there. The Resistance Member will confide in you that he needed the YoRHa chips to fix up an android body that he had found, with the hopes of creating his own family.
Once you leave the area, you will receive a notification from Command that the YoRHa android and Resistance Member were sadly both killed by machines. This completes the quest in your log.