Once 2B is mobile again, check in front of you for an item box containing a Skill Salve S. For the next objective, you have to first obtain a dynamic scanner to be able to detect signals from YoRHa survivors. Go speak to Anemone at the Resistance Camp and she'll point you to Davola and Papola. Go ask them about the scanner and they should hand it over with little fuss.
Equip the program to a pod and return to the Flooded City to start searching for survivors. There are three YoRHa members you must find here. Two should be in plain sight on the ruined roads while the last one is hidden behind one of the buses. Use the scanner to pinpoint her exact position. The soldier should give you a lead on where 9S may have landed, so use the access point and travel to the cave over at the city ruins.
Follow the path forward until it forks then go right to the elevator which leads to the Copied City. Follow the marker to the destination while making sure to pick up all the shiny things you come across. Also check for android bodies to harvest for plug-in chips and at one of the dead ends in the area is an item box with a Large Recovery.
Waiting at the destination is Adam who you must defeat twice in order to accomplish what you came here for. The first phase of the encounter isn't so bad as Adam's moveset is very limited and predictable. He won't do much besides teleport and throw blocks.
The second phase is where things get somewhat complicated. You'll definitely wan to take a more cautious approach here and counterattack only after Adam has made a move. Try not stray too far when you dodge either so you can hit him back quickly too. Attack with the pod's guns if you can't get close. Abandoning 9S after the boss encounter will unlock Ending I.