Head downstairs and collect [2 REVOLVER AMMO (E/N/H/S)] plus the [FIREFLY ORDERS (ALL)] from near the body next to the stairs. Move the container to the gate and head over to proceed. Simply follow the main thoroughfare and wade through the shallow water until the Capitol Building rises up to your right. Before going that way, hop over the fence of the chapel to spot a [FIREFLY PENDANT (MELINDA DAVIDSON - 214)] in the water. Head inside the building to trigger a scene.
Firefly Pendant Melinda Davidson
In the next hall, search the table for [(1/2) ALCOHOL (E/N/H/S)] and [(3/4) RAG (E/N/H/-)], then head up the left stairs. Move through the hall, past the balcony and make haste from this point onward. In this room, collect [(1/4) BLADES (E/N/H/-)] from the left side near the windows and [(1/2) BINDING (E/N/H/-)] from behind the desk to the far right, along with [5 SKILL PILLS (E/N/H/S)] on top of it, then drop down to enter the adjacent building. Collect the [HUNTING RIFLE (E/N/H/S)] from the body and move into the hall.
Two enemies will start searching this hall. Hide behind the crates to the left and wait for the first to move into the room to your left. As soon as he's gone into that room, move around the left side of the pillar in the center of the main hall and wait for the second guard to pass (past the right side); curve around to strangle him quietly, then head inside the room to the left in which the first guard went looking.
Depending on if you make a sound or not (for example by touching the object behind the cases) the guard will inspect this room faster; you can strangle him if you do everything correctly, and the same applies for the other guard who will soon inspect these rooms. That leaves just the one last guy in the hall; dispatch him however you please. Don't forget to collect the [5 SKILL PILLS (E/N/H/S] from the desk in the small room furthest down the hall (still on the initially left side of the main hall). At the end of the hall, head downstairs and drop down.
In this area, quickly collect a [RAG (E/N/H/S)] and [(3/4) BINDING (E/N/H/-)], then head inside the first doorway and enter the room to the right to find a [HEALTH BAR (E/N/H/S)]. Move to the end of this room and hide behind the table until one of your enemies enter the room; curve around the room quietly to strangle him. Soon enough, a second one will enter this room so prepare yourself for it and strangle him as well. One other will investigate the halls, allowing you to take him out fairly easily.
Approach the next hall from the right side of the area; there are three more enemies searching the place, one of whom is usually in the room to the right; he can be strangled fairly easily by hiding behind the bookcases (but be sure not to kill him too close to the exit furthest away, or one of the others will spot him). There's also a [HEALTH BAR (E/N/H/S)] on one of the benches here. You can sneak by the remaining two enemies, but if you must, sneak behind the one closest to you as he's walking away from you and while the other is further away. Do take out the last one quickly.
Tip: Don't bother healing Joel with a Health Kit, especially not if you're playing on Survivor. His wounds will be healed not too long from now.
Back outside, head down the subway stairs on the left side of the street/river and rush down. In the corner immediately to your right, collect the [(1/2) ALCOHOL (E/N/H/S)] and [(1/2) BLADES (E/N/H/-)], then move down. As soon as one of the guys closes in on Joel, curve around the object to strangle him. The other guy will come to inspect this place soon enough, so be prepared to take him down as well.
Follow the subway tube until you reach a flooded part where Joel will need to swim to continue onwards. Ellie will take the small walkway on the side of the area. Soon enough, once you've dived underneath various heaps of rubble, you and Ellie meet back up and she'll find a working flashlight. Grab the [SMUGGLER NOTE (ALL)], then dive and swim through the small hallway and climb back up to find [5 SKILL PILLS (E/N/H/S)]. The flooded storage room contains [PARTS x4 (E/N/H/S)] and a [FIREFLY PENDANT (SHIYAO JIANG - 178) (ALL)].
In order to continue, head back to the main tube and grab the raft floating somewhere in the middle of the area in order to transport Ellie to the other side; she'll in turn lower a ladder for you. Simply head upstairs around the corner to exit the subway.
Note: All of Joel's injuries will be healed after the next scene.