"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. 

To achieve “Big Boss” 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. 

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