"The game tracks kills and alerts on a checkpoint basis - during a multi segment speedrun you can save and quit upon discovery or accidental kill if you don’t enter a new area first. You cannot save & quit a continue screen. 

Achieving “Big Boss” rank requires you do not kill anyone - however there are instances where a “kill” does not count towards your score. Such as Ocelot - because he is not killed during your encounter lethal means are allowed during a Big Boss run. Knocking guards over the railings in the Underground Base do not count. They do count in Nuke Building 1F.

Soldiers killed by exploding barrels do not count towards your end score, required to successfully clear the Escape Route. 

...It is indeed a requirement that you play with Game over if Discovered condition turned “on”. 

• Not up to date, but a decent baseline for Mantis

Return to Metal Gear Solid: The Twin Snakes