uh, excuse me, but Big Boss' weapons are super-accurate from the 60's and so I do not believe they could take out future jets. Allow me to show you this wikipedia article about cold war-era weaponry to explain
Also, to summarize DDS' story, Cielo wanted to die and he doesn't actually "die" from that anyway so take that how you will.
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You beat yourself up with your past. Don't blame yourself, blame the world. Blame God. Blame me.