Well, that complicates my theory, but it might still be workable...
If an unsilenced gun were fired on the base, how far would the sound travel?
In the mean time, here are the theories I've already prepared.
Meryl Silverburgh was killed by sarin gas that had been pumped from a gas grenade into the gas stove, such that when the stove were turned on, the gas would fill the room. By the time the door was opened, the gas had already gone out the open window.
Naomi Hunter was killed when she was thrown from her jeep, which the culprit had sabotaged well ahead of time. The warning lights weren't on because they were also sabotaged.I plead Knox's 4th for any specific details on the sabotage, I don't know much about cars. Maybe they weighed down the tires so that the car would stop quickly once the engine gave out?
The culprit placed the cactus covered in venom on the floor of the shower, then used soap and/or shampoo to create a slick spot which Solidus slipped on, landing neck first on the cactus. The slick was washed away by the shower
The culprit used a rubber band (or multiple rubber bands) to fling the stake at Solid Snake like a slingshot.
Gray Fox's jeep was also sabotaged ahead of time, with the emergency lights shut off. The steering wheel was tampered with, such that a small steering adjustment sent Fox veering out of control.
Also sabotaged in advance: the gas stove again. The culprit removed the stopper, so that turning on the stove instantly flooded the room with a large amount of burning gas, which set Johnny Sasaki on fire, then quickly burned itself out as all the gas was used up at once.
Ocelot's jeep was sabotaged so that the gas tank would explode. Or maybe the culprit rigged a grenade or plastic explosive to it before all the equipment was collected, but I'm pretty sure that violates the red.
Big Boss was killed, then the culprit slowly hacked his head off with a semi-sharp object that wasn't among the weapon blades thrown away, such as the tent stake.
The culprit strangled Miller to death on the roof, then climbed down a rope - not to the bottom, which would have taken too long, but to Big Boss's office, the window of which was broken after Erika ran upstairs. The one who broke the window was the accomplice, who was hiding in the restroom. The two of them quickly retrieved the rope together.
The culprit is Sniper Wolf. The accomplice is Vulcan Raven. According to the meal schedule, only the two of them working together could have entered the kitchen to sabotage the stove on two separate occasions.
And as long as we're here,The Philosopher's Legacy is in the rose patch in the courtyard, the center of the Command Platform, where all the paths on Six House Island connect. Big Boss and Ocelot's secret talk was about it, which is why they had their talk there.