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.
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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.
