The Pitt is split between two factions: the raiders run by Ashur, and the slaves led by Wernher. Werner recruits you to help free the slaves from Ashur's control and steal their in-progress cure for the plague devastating The Pitt. This disease transforms people into mindless Trog mutants and is completely lethal to children. This is why Ashur acquires slaves to work The Pitt's industry; it is the only way he can sustain and repopulate the city in its current state.
After earning your freedom, you have the opportunity to meet Ashur himself and slip in to steal the cure. Even before you speak with Ashur, and before he even notices you, you overhear part of a conversation between Ashur and one of his chief underlings, wherein the underling says "slaves" where Ashur insists they say "workers". I'm a strong believer in the idea that good people can be brought down by the people around him, and from my perspective, Ashur's dreams for The Pitt are hindered by the raider mentality of his main forces.
In addition to this, Ashur reveals to the player that he knows about Wernher and his hidden motives. Wernher was once Ashur's lieutenant and had attempted a coup, but failed and was enslaved with the others. This calls into question whether or not Wernher is truly fighting for the slave cause or if he's just using them for payback and a second shot to gain control.
It is at this point the slaves rise up and Ashur leaves to quell the uprising. You use this opportunity to slip into the cure development lab and swipe it. There you discover the truth: the cure is an innocent baby girl, Marie. She is Ashur's daughter, miraculously born with an immunity to the Trog disease, which her scientist mother is carefully developing a cure from. When the cure is perfected, Ashur intends to spread the cure to everyone, allowing The Pitt to prosper without the need for slaves.
There you make the big choice: side with Wernher by stealing Marie and killing her parents, or side with Ashur by leaving Marie alone and confronting Wernher.
After a lot of thinking, I sided with Ashur. Part of it was roleplaying; as "Good Karma" as my character was, he couldn't in good conscience rob Marie of her parents, knowing too well the loss of his own. More than that, I couldn't foresee a good future under Wernher. Cure development under a skilled scientist with Ashur, or with Wernher, who hands her off to some emancipated slave woman with no idea what she's doing? I felt that either Marie would be harmed due to reckless development or nothing would come out of it. Furthermore, I didn't trust Wernher to be a good leader; I absolutely NEVER trust vengeful rebels to be better than the people they overthrow.
Does this mean I advocate slavery? Hell no. However, I'd rather reach a bright future through dark actions than have good actions lead to a dark future. As far as I'm concerned, The Pitt is doomed without Ashur and his family.