- Major Zero is the founder of the Patriots. (In a way, we knew this from Portable Ops.)
- He formed the Patriots to honor soldiers like The Boss. He recruited Para-Medic (Dr. Clark, whom Grey Fox killed on his escape, revealed in MGS1) and SIGINT (DARPA chief Donald Anderson), and eventually Big Boss, Eva and Ocelot become members temporarily.
- Zero becomes corrupt and clones Big Boss without his consent. Big Boss finds out and leaves the Patriots. Eva and Ocelot become intent on destroying the Patriots. Instead of recruiting more members Major Zero uses AI automation to form the rest of the Patriot members so that his system became automated by smart A.I.s.
-Naomi dies from cancer after her nanomachines are disabled
-Vamp dies after his nanomachines are disabled, then Raiden finishes him off.
- Eva dies trying to save Solidus' body in a fire because she believed Ocelot was really taken over by Liquid. Snake tries to save her but his face gets badly burnt.
-BIG BOSS IS STILL ALIVE. How the fuck?
- Big Boss dies by deliberately breathing in the mutated FOXDIE injected into Old Snake by Drebin (the arms dealer). He appears to Snake in a graveyard and stops him from killing himself.
- Big Boss kills Major Zero at the graveyard. Major Zero was practically dead already, he was just alive in a physical sense at that point.
- Ocelot dies.
- Ultimately, the story of Metal Gear Solid 4 is the conclusion of a vast conspiracy through which Ocelot and EVA (with Naomi's help) exact their revenge on Major Zero, and open the doors of redemption for themeselves. We should be under no illusions as to the true role of Ocelot from the very start. As Big Boss reveals, "In order to fool the system, Ocelot used nanomachines and psychotherapy to transplant Liquid's personality into his own mind. He used hypnotic suggestion to turn himself into a mental doppleganger of Liquid." Foreseeing every step Snake would make, every likely outcome, Ocelot allows his apparent adversary to complete the most integral parts of his plot because he understands fundamentally that Snake is the tool of the Patriots, and therefore above suspicion in their eyes - whether he knows it or not.
- Ocelot reveals that he was a "doppelganger" of Liquid Snake to throw off the Patriots -- Liquid's arm never truly took control of him.
- Snake lives but has 3 months to live, so he goes off to live the remainder of his life in solitude.
- Meryl marries Johnny Sasaki.
- Raiden doesn't die and reunites with Rose and his kid.
- In a sense, Solid Snake was the villain all along. He was the "gun of the Patriots." He has always been a tool of the Patriots.. during MG1, MG2, MGS, MGS2, MGS4 - he was created by the Patriots. They made him age extremely quickly and made him sterile because he could have fallen into enemy hands. He will die alone, isolated from the world months after MGS4's ending, knowing that he was always a tool of the Patriots.