He didn't die in MGS3. He did kill The Boss, which is probably what you're thinking about, that's how he earned the codename Big Boss.
Big Boss never actually died. He was ostensibly killed by Solid at the end of MG2, but was kept alive by The Patriots in a coma until the end of MGS4(EVA had previously retrieved his body with Raiden's help and rebuilt him using parts from Liquid/Solidus however he was still in a coma until The Patriots system was taken down).
Timeline is: MGS3, Portable Ops, Peace Walker, MGSV, Metal Gear, Metal Gear 2, MGS1, MGS2, MGS4, and finally Rising if you want to count that.