The entire time I thought I was playing as Big Boss was me playing as a member of the medical team?!!!! Not the combat team, not the security team, not the base development staff, not the support staff, but the FUCKING MEDICAL TEAM. *Scust at this BS* I'm building a PMC thinking I'm battlefield Jesus but instead I'm a lesser being. How would Big Boss handle these missions? I doubt he kills Quiet and lets Huey on the base at all.
Those flashbacks and flash forwards in time screwed my head up but let's talk about the implications for the series moving forwards... SPOIL, SPOIL, I'M SPOILING GOTDAMMIT.
I refuse to believe Zero, Chico, Paz, Sigit, the Medic, and Big Boss are dead. The tapes mention how Zero was in a secure location in Hell's Kitchen. "Paz" or whoever she really was met with Zero there. Now here's where my theory starts. Zero gave Paz the Venom Snake treatment as she left the base only this time he didn't have to wait 9 years. He mentions how there were eight other candidates there for the role of "Paz". How do we know he didn't Venom Snake her (fake her death and use body double conditioned with her memories) and allow her to return to life as a student while fake Paz lures Skullface to his location? Yeah, Paz is alive somewhere and could come back for MGS 6. This gets to my next part in theory.
If Zero's location was so secure and he could move any time he wanted. Then how do we know he was there in the first place for the meeting with Skullface? For all we know Zero used body double to meet Skullface and survived through the body double taking the fall thanks to Cipher trickery. According to the tapes Cipher already had information control in place at this point in time. You might say we saw him die in MGS4 but nah, body double + hypnosis + nanomachines.
If the Patriots could revive Big Boss and keep him alive secretly then Chico made it out of the plane crash alive too. Remember Kaz mentions Chico died in passing to VS but we never see Chico's dead body. I can easily see a scenario where Chico wakes up after his 20 year coma with a recording from Big Boss and Fake Major Zero telling him to lead the new world's soldiers.
Sigit had access to information control and nanomachines so he's not dead. Matter of fact he was on the mission when Big Boss faked his death at one point so he's not dead either. Dr. Clark had access to years of research on rebirth and death so she survived as well. The end of MGS4 proves the Patriots are alive and well thanks to the reveal of Rat Patrol 1.
TL;DR If anyone can become the best soldier in world history thanks to hypnosis and a body double then it stands to reason that this logic extends to major players in the story. If Zero had enough time to plan ahead for this scenario then he had enough time to cover everyone else. Additionally, Cipher had time to keep themselves alive through everything thanks to this example.
As for MGS 6. It could take place in an era where militas rise up thanks to the legacy left behind by Snake and Big Boss. We're Chico with his right hand man Raiden leading the charge against everyone mobilizing Metal Gears while Solid takes the role of Colonel Campbell.