The Patriots have come to understand, like Big Boss at the end of MPO, that certain individuals will always need war. But The Patriots also want humanity to progress, and war can make this progress unpredictable.
Big Boss (MPO)The meaning of justice can change from one day to the next. A professional soldier never brings justice into the mission. The only ones who need a reason to fight are the ones who fight for a living. That's what my mentor told me. Politics are fickle. They change with the times. So long as we remain loyal to our countries, soldiers like us need nothing to believe in. She died out of loyalty - not to justice, not to her country. To herself. For the mission.
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I'm not living unless I'm in battle. So I have to find my own reason to fight. I have to pass on what's been handed down to me...
So The Patriots have decided to take CONTROL of war. To manage it. Their goal has been to be the ones behind every conflict; to be the ones that will instigate all conflicts, judge all conflicts, and to end all conflicts, because war is a potential threat in their grand scheme, but one that will always exist.
By taking control of war, war would never hamper humanity's progress because it would be constantly regulated, and soldiers would always have a place to fight. They can chose their sides, fight for what they believe in, even tho in the end the motivations behind the wars are fabrications. They never need to know the truth.
In MG1 and MG2, The Patriots seized an opportunity (or instigated it). They wanted to see if they could monitor, regulate, and end a conflict that threatened their rule. It was a success. The fact that this conflict was started by a potential member of The Patriots raises questions that will probably go unanswered until MGS4. It's possible that Outer Heaven and the Zanzibar Uprising was merely a test case, with Big Boss serving his final mission in the same way The Boss served her final mission. He would be known to the rest of the world as a traitor who attempted to unleash a nuclear war, when in fact he simply died for the mission. Hence why in MGS4 we see that his grave (if it's his) is identical to The Boss' grave. He served the same purpose, to the same people. But it is possible that just like The Boss, he died empty, unable to fulfill his true dream, and passed the torch to his successor, hoping that Solid Snake would not be a prisoner to fate as he and his mentor were.
In MGS1, a conflict similar to the one in MPO emerged, a conflict not started by The Patriots, but by a rogue soldier; Liquid Snake. Their former insurance policy was used, Solid Snake, whom had been developed during the Outer Heaven/Zanzibar incidents, and the conflict was controlled and ended, once again under the supervision of Roy Campbell.
In MGS2, The Patriots develop a method to control the flow of information, a method similar to the one they developed to control war. They trigger a conflict, observe it, manage it, and end it, through the use of information. By the end of the exercise (again under the supervision of Campbell, altho an AI version), they finally achieve complete control. They are now in control of humanity's progress and they can deal with the emergence of any conflicts that would threaten their rule.
By the time of MGS4, war has finally been entirely regulated, thanks to The Patriots:
Solid Snake (MGS4): War has changed. It's not about nations, or ideologies. It's not even about profit, resources, or ethnicity. It's an endless series of proxy battles, fought by mercenaries and machines.
War, and its vast consumption of human life, has become a rational, well-oiled business transaction.
War has changed. ID-tagged soldiers carry ID-tagged weapons, use ID-tagged gear. Nanomachines inside their bodies enhance and regulate their actions.
Genetic control... information control... Emotion control... Battlefield control. Everything is monitored, and kept under control.
War has changed. The age of deterrence is now the age of control, averting catastrophe from weapons of mass destruction. And he who controls the battlefield, controls history.
War has changed. When the battlefield is under total control, war becomes routine.
The Patriots have achieved their goal. They are in complete control of human progress and can prevent any conflict from going out of control. Their system of information control enables them to filter the evolution of mankind, and their system of battlefield control enables them to keep war regulated; to make it nothing more than a routine part of a grand system of control. Even the world economy's balance relies on it, according to Campbell.
War continues endlessly, but is under complete control and hence human progress remains on track, under their supervision. Those who start conflicts are nothing but puppets in a grand system of control. No one is truly fighting for their causes anymore. Everyone is fight with the: Guns of The Patriots.
What will Solid Snake do? He is sent to eliminate Liquid, under the supervision and command of Roy Campbell, once more. If he erases himself from existence, him, his genes, his memes, then The Patriots lose and Liquid-Ocelot will succeed in throwing a wrench in their system of control, causing the world to fall into ruin, but at the same time freeing the world and leaving it to decide its own future. Will he do it?
Elisa (MPO): Your son will bring the world to ruin... Your son... will save... the world.