The Factory Zero achievement is not about saving people. It's about adopting a particular playstyle.
The achievement is as follows:
You survived The Missing Link using no Praxis kits, weapons, or explosives. Whoa.
This means:
- Do not allocate any Praxis points, whether acquired through levelling up or after collecting a Praxis kit
- Do not fire any weapons
- Do not throw grenades or place mines or other explosive item
You can however, use environmental explosives (throwing explosive barrels), use items that give you health, buy or sell any items, equip/aim/reload weapons. You can also set off alarms or make people suspicious. Regarding not firing weapons: takedowns (both lethal and non-lethal) are not considered weapons and can be used freely.