For each mission, make sure to be loaded up with plenty of sleep darts. Choke out any enemies in your way and dart any enemies that are facing you or if they’re too far away to reach. Make sure not to hit enemies in the head with sleep darts, it will kill them. Darting enemies that are standing on high ledges or near water may cause them to fall and die, so be careful. For each mission, there is a non-lethal way to handle all main targets:
Mission 1 - A Captain of Industry: After interrogating Rothwild, you are given three options. You can either prepare him for the crate or leave him in the chair; both options will keep him alive.
Mission 2 - Eminent Domain: Meet with the prisoner after entering the legal district. Go to his apartment and take the required items. Unlock Apartment 10 and pick up the odorous bag. Locate Timsh in his estate and pickpocket him, which will switch the forged letter you have with his letter of immunity. Enter the basement of the estate and place the odorous bag in the ventilation system. Wait until Timsh is neutralized, then finish off the mission.
Mission 3 - The Surge: Knock out any Overseers in your way, including Overseer Hume. At the end of mission, choose to capture the remaining Overseers and spare Billie Lurk’s life, assuming you have completed the game in Low Chaos up until this point.