Don't let NPCs raise the alarm.
Don't let NPCs see you as you shoot someone.
Don't let NPCs see another NPC being shot. (Ok if one get shot when the other is looking away, but watch out for those peeking from the windows)
Use Overload function on power charger to kill NPCs "stealthily" from behind.
Crouch and sneak behind NPCs (you can basically crawl up to 0 distance without suit upgrades and they won't turn around...oddball) to kill or steal their IDs.
OR
Disable the settlement alarm, before going nuts.
Even if settlement alarms are not raised, if they are red on the radar screen, it means you botched it.
Other tips:
- NPCs only get alerted once. If they see a dead body or cut door panel, they go yellow once only. If they don't see you, they will go back on their way and won't bat an eyelid again at the same "problem".
- So you can cut a panel, run away, wait a bit and come back after NPC went on their way. Can even chat them up in front of the body if you like.
- If you trigger a scan, you can drop items, remove cloned profiles to avoid the alarm, as long as they haven't started the scan. You can pick up the contrabands you dropped after NPC is done with the scan.
- Some CMD buildings have an unguarded door in the back.
- You can lure NPCs out of buildings if enough of a commotion is raised. Explosions or killing NPC works.
- Use the Apex service. If you get killed, no rebuy cost.
- Don't start a stealth mission if you have a fine or are wanted.
For an out of game final solution...
1. Finish the mission objectives except the "Leave Settlement" one.
2. Log out and back in to reset settlement. This turns all hostile units, non-hostile...cheating but w/e...
-> This removes all items on the base except the power regulator
-> Settlement state reset to beginning. (NPCs come back alive, alarms turned off, no longer hostile)