Snake survived Ac!d, and is alive alongside his clone in Ac!d2.They say that Snake died following his fight with the Metal Gear, but they at no time mention his body or how he died, only that they got the material from the Gear's remains, nor do they mention Teliko. Snake was forcibly pulled out of retirement, betrayed countless times, and had his memories messed with, and wanted to retire again. The odds being, he probably decided to fake his death and disappear. The government thinks that Snake's dead, can't find him, but find some of Snake's blood from the Gear battle. So they make a clone out of it, because why not?No one doubts Snakes "Death" because the clone's around, and Snake himself is not going to poke his head up when another him's running around that people think is the real deal. Snake and Teliko are off chilling somewhere else, while conspiracies and governmental jerks are messing around with his clone. Snake is probably not even aware that he's been cloned.
Alice's ghost possessed Teliko and Alice!Teliko ending up killing Snake.