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Free Labor Preparation
Uptown has a lot to offer, but we're focusing on the quest at the moment. You need to think about your decisions too, since it will change your required preparation.
If you plan to side with Wernher and the slaves, then you should take about 10 minutes and walk around Uptown. Figure out where each catwalk goes and where the doors are. There will be two major battles in this area. Getting lost won't make them easier. If you plan to side with Ashur, then don't worry. Just go find him in Haven.
As to the actual decision, I'll note that Bethesda considers the two sides neutral. Wernher isn't an angel. The cure is Ashur's baby and he wants to risk its life to find a cure and make a power grab. Ashur isn't a devil either. Ashur seems to genuinely wish to free the slaves as soon as a cure is found. So, you're free to make a choice. It's basically karma neutral and the rewards are essentially the same.
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Siding with Wernher
If you plan to do this, try to pickpocket the ammo off of all the raiders. It makes the rebellion much more successful. Go into Haven and talk to Ashur. You can try to lie about knowing Wernher, but it doesn't change much. He feels his case is strong enough. You can fight him here and now, but that's a little pointless. String him along until Krenshaw sounds the alarm about the slave rebellion. Walk over to the lab and talk to Sandra. Choose to kidnap “the cure" by either activating Marie or choosing the appropriate conversation choice. Kill Sandra and any of the raiders nearby.
Then just fight your way out. There isn't any real science to this. Just backtrack back to Midea's with Maire. There will be at least 5 slaves with auto axes, and they can at least wound and distract the raiders. Keep moving forward. You don't necessarily have to clear the area either. Wernher has a plan for them. Just get to Downtown. You can take the Mill path for simplicity. There will be more slaves inside who are able to deal significant damage to the radiers.
Go to Midea's house and hand over the baby. She'll tell you about Werner's hideout. He's behind a newly opened door in the steelyard. Go over to the steelyard and move straight forward from the entrance. Go up the stairs and towards the back. You need to get past Wild Bill's corpse and make it to the Wildmen's shack. There should be a slave on guard and a bright light above it. Go inside and talk to Werner. He'll give you the key to the underground and tell you his new plan to unleash the trogs on the raiders. He'll give you a stealth boy to help with your escape.
Go back to the train cars and look for the sewer entrance to the power plant. It's marked. Follow the linear path and kill all the trolls. There are several groups of trogs in various locations along the catwalks and machinery. Just keep grinding through the masses. The auto axe is quite effective in these narrow spaces, but the shotgun is naturally effective too.
Just get to the end of the fairly short path and access the computer here. Use it to kill the floodlights in Uptown. Go out the nearby exit to end up in Uptown and watch the carnage. Ashur shows up at the exit to try and stop you. If you didn't kill Sandra for some reason, then she'll be here too. You can either kill them or just run away and let the oncoming group of trogs do it. Either way, make sure you grab Ashur's armor, since it's pretty nice.
You can try to fight the trogs. It's possible to win if you just fire and run. There are also a good number of sniper's perches which they can't access. You can just use the stealth boy to avoid most of them though. They aren't too perceptive. Uptown will be locked off once you exit anyway.
Get back to Downtown through whatever means possible. Midea and Wernher should both be at her quarters. Talk to Wernher to be declared the new boss and complete the quest. You can now use the ammo press in the mill. Midea will also now buy teddy bears for Marie.
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Siding with Ashur
This is quite easy really. Talk to Ashur and agree to help him. Then talk to Sandra and walk out without kidnapping the baby. Go outside and watch the raiders mow down the slave rush. You can help out if you want bad karma. Go back out to the Mill. You can just hang back and let all of the raiders inside the back areas rush out to meet the slave attack. It's a fairly cool fight to watch from the upper level.
After that, just calmly walk to Midea's quarters. You can either pass a speech check or grab one of the notes on her desk to find out the location of Wernher's hideout. Go to the steelyard and head straight back. Go past Wild Bill's body and past the Wildmen's shack. Kill the one slave on guard duty and go inside. In my case, Wernher was already hostile. If you go in without a weapon drawn, then you might have better luck. You can use the Black Widow perk or pass a speech check to convince him to leave. Otherwise, just defend yourself. He is leveled to your character, so he might be incredibly strong. Just use your new weapons to wear away at him and win. Loot his body and report back to Ashur at Haven. Things are back to normal and you can now use the ammo press. Sandra will buy teddy bears for Marie.
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Aftermath and the Ammo Press
The Pitt will still be open and functioning in a similar fashion regardless of your choice. The slaves still go through their work routines if you free them. The only real change is the noticeable lack of raiders in the event of a rebellion.
Marie's caretaker will start up an unmarked quest for teddy bears. She'll buy them for 30 caps a piece with 10 experience points as a reward too.
Finally, the ammo press is all yours. The ammo press is inside the mill. You can find it just past the large cage that looks down into The Hole. You can also look for the two steel crushers that have a terminal near them. The operation is fairly simple. You can load unneeded bullets and scrap metal into the material bin. Each of these has a relative value, with some more “expensive" bullets. For example, it takes 15 5mm bullets to make a .308 sniper round and vice versa. Just load your ammo up and use the terminal to make the bullets you want.
The real value is that most people should have accumulated a whole lot of useless ammo from their wanderings. The ammo press can take all of those 5mm rounds your sniper doesn't use and turn them into .44 bullets for Lincoln's Repeater or .308 rounds for your favorite rifle. You can always return to The Pitt through fast traveling to the tunnel, activating the railroad car, and fast traveling to the Mill. Keep this in mind.
That's it for the main questline of The Pitt. Congratulations.