One way in which Metal Gear Solid V contributes to the overall saga, and the one that will be the sole focus of this post, is by shining a light onto the true nature of the relationship between Zero and Snake; this has been exposed before in MGS4 and Peace Walker, but the revelations in Phantom Pain drastically changed my own reading of the facts. There will be spoilers ahead, so please stop reading now if you haven't finished the game yet and wish to experience this by yourself.
If you've played the game to true completion, you'll know Big Boss and Venom Snake are actually two different people. For this post, I'll be mainly grazing on the material that directly affects Big Boss in the game: the prologue/epilogue and the audio tapes. I'll focus on how the material in MGSV takes a "show, don't tell" approach by building on previous work in the franchise like the initial reason Zero and Snake split up and the ideological rift that formed between them after Peace Walker. This hypothesis is based on my own analysis of several key moments within the franchise and I welcome any criticism towards it in an attempt at digging deeper into the lore and extracting more meaning out of the work done by Hideo Kojima, creator of the series.
First, it must be said that Zero and Snake were friends. They operated together in FOX and even founded the organization that would be known as Cipher, and subsequently the Patriots, together - though it may not have been named as such at the time. But it should be clear Zero didn't see Snake exclusively as a friend: he was a symbol, and an important asset in the scheme Zero had put in motion in the aftermath of the Boss' death. Fearing Snake might not share his perspective on the way the world should function, he had Snake cloned in an attempt at securing what Zero perceived to be an asset. As Snake himself put it, the children weren't the problem, but what they represent: mistrust, manipulation, betrayal and ruthlessness - not to mention the basic violation of his individual traits. Zero was willing to engineer a human being to take Snake's place in case he did not comply with the plan. This led to Snake's departure from the organization he and Zero had founded with EVA, Ocelot, Clarke and Anderson.
But even before all of that, in the year 1964, during operation Snake Eater, Snake executes the Boss as the final objective of his mission. He manages to carry out the deed, but his strong feelings for her make him feel conflicted about the whole affair. His inner conflict turns into extreme guilt once the truth is exposed by the spy EVA: her defection was initially a ruse, but her operation was compromised when Volgin fired the Davy Crockett in Russian territory. America needed to present tangible evidence of its innocence by dealing with the defector that supplied the rogue colonel with the warhead. This would help Khrushchev maintain power and avoid all out nuclear war. Thus the Boss' objective was altered: in addition to her current objectives, she would be required to die. The world could never know about her last mission, she would die and be remembered as a traitor who almost sparked a nuclear war. In the end, she wasn't a defector. She was a loyal soldier who carried out her mission perfectly regardless of personal cost, or Snake thought.
Snake saw the Boss as the perfect soldier: every mission she ever undertook, every order she ever accepted, every objective she ever accomplished defined her in his mind. He couldn't see past her profession, couldn't acknowledge any other facet of her personality and the fact that being a soldier might not have been her entire life. Even though she was a woman of many talents, as evidenced by Strangelove's accounts in Peace Walker, Snake saluted and cried for the Boss, the woman who he thought had soldiered on out of duty as she was a given a suicidal objective in Snake Eater. She was 'loyal to the end', to her mission. Snake didn't understand, at least until 2014, that 'loyalty to the end' actually meant loyalty to your own beliefs: the Boss carried out her final objective so humanity could live on unscathed in the hopes that it would one day come to the same realization she had when looking back at the Earth in space and not because she felt duty bound her to those orders. The Boss desired peace for humanity, that meant she didn't want to risk humanity being victim of a senseless nuclear war. She accepted her objective because she believed the best chance humanity had was for her to take the blame for that Davy Crockett going off in Russian territory and allow America to use her death as proof they weren't to blame.
The Boss' exchange with Snake in the beginning of Snake Eater shows her outlining several 'problems' with the orthodox definition of a soldier in a veiled manner. She criticizes Snake for showing feeling for comrades, saying that is a sin for a career soldier and that such a soldier should be loyal to his country, and yet, when Snake points out he is loyal to his country despite who's in charge, she points out how futile that is as the times truly dictate how politicians feel and think.
Peace Walker's first ending shows Snake denouncing the Boss as a soldier who had given up on her entire life. This is in response to the revelation that the Boss aspired for peace, that she aspired for humanity to come together as one and forget all notions of segregation that kept humans apart, such as geographical borders. This revelation, of course, was enabled by the Peace Walker AI, which was trained to follow The Boss' rationale; similar to how the Patriot's AI network was trained to follow Zero's rationale, or even how Venom was conditioned to think like Snake. The accuracy of such revelation is, therefore, questionable and imperfect. However, as questionable as that conclusion may be, Snake took it to heart: it struck a serious psychological blow to Snake, but it also presented him with an opportunity. It struck a blow because it conflicted with his version of reality by destroying his narrow perception of who the Boss was and what he thought her rationale was, which was a basic building block for Snake's identity; however, it also presented him with an opportunity of ridding himself of the excruciating guilt he had felt for almost a decade. Guilt born out of the shame and disappointment he felt for killing who he perceived as the best soldier who ever lived, and probably the person he loved the most, because of a lie the government fed him.
In order to salvage his identity and rid himself of guilt, Snake blamed the Boss as a defence mechanism. In Peace Walker's first title card dialogue scene, Snake states the Boss betrayed him. That in putting her gun down, an euphemism for seeking peace, she had given up everything she was up to that point, including him as an apprentice during her years as a soldier. It is much easier, and a much more comfortable proposition, for Snake to lie to himself and interpret the Boss' actions as betrayal, than it would be for Snake to come to terms with reality. The truth could, in fact, end up making him feel even worse about killing her, seeing as she was such a noble and determined soul.
He goes on to tell Kaz he "won't make the same choice" she did. This statement demonstrates he's willing to stand by what he currently believes in, despite the fact that the seed for his own rationale may be based on a misconception. In practical terms, this means he'll go deliberately against what the Boss was for in an attempt to further invalidate her in his mind: he won't aspire for peace like she did. In fact, as time would reveal, he fights for the exact opposite: Snake desires perpetual war.
The reasoning he fabricated behind such an excuse, though the character himself might prefer calling it a stance, is that a peaceful world would have no place for soldiers like Snake and that would mean an end to his lifestyle. So he validates his selfish decision of opposing peace by buying into the cause of preserving the warrior's lifestyle and the status this group has achieved within society at that time. This is, of course, the role which Snake most intimately identified with, to the point of actually confusing it for his own identity. This is explored further in Peace Walker itself and even outright exposed by the character in Metal Gear 2: Solid Snake.
The fabrication of such a thought process to support a perspective designed to alleviate his guilt and the impact of the revelation that the Boss was not who Snake thought she was shows how strongly Snake’s own identity was rooted in who the Boss was. His life was the military and, perhaps, his most important years were spent with the Boss; she shaped who he thought he was and he took her as his role model, as his idol and maybe even his muse. When placed under mental duress, Snake retreated into the importance of his duty as a soldier, all the while giving up on himself as a man. The transition was probably easy since he was already incapable of separating himself from that role, it had almost completely fused with his own self-image; except the soldier didn’t have to deal with Snake’s problems and traumas. The soldier could just shut all of that out and deal with the task at hand, the task of hating the Boss and not dealing with what she meant for Snake as an individual. So he chose to drop all other aspects of his own identity and architect a dream based on the most intimate persona he's ever had to play in his life.
Desiring war, under the pretense of protecting the soldier’s lifestyle, means fighting against peace. The peace the Boss envisioned for the world. Striving for that allowed him to oppose the Boss’ true self, one that conflicted with his own warped image of her, and shift his perception of her from a hero to a villain. Ultimately, this enabled him to achieve two things: stop feeling guilty over her death and avoid dealing with the misconception of her identity.
With this knowledge, we loop back to the moment Snake woke up in 1984 and was informed by Ocelot that his best soldier had been brainwashed into a doppelganger by his former friend (now perceived enemy, due to the events of Peace Walker) and that this same man had been, at the same time, connected to both the incident that took 9 years of life and his survival during that same period. Throughout the Metal Gear saga, the concept of the Patriots was introduced in Metal Gear Solid 2 and tied in to the events of every other game in the series. In Metal Gear Solid 3, we met a whole new cast that, for better or worse, mimicked the one presented in the original PlayStation game launched in 1998, which in turn mimicked the cast of the two previous games in one capacity or another. In June 2008, with the release of Metal Gear Solid 4, players were given the truth: both storylines were connected and that group presented in MGS3 were the original members of the organization now known as the Patriots.
One must understand that, for almost 7 years, with the inclusion of events depicted in Peace Walker, players were led to believe Snake and Zero had parted ways in the early 1970’s and that, since then, they had been waging a secret war that ended up shaping the world into what it was in 2014, when Metal Gear Solid 4 takes place. However, Ground Zeroes and the Phantom Pain both reveal a much more nuanced truth about the alleged “war” between these two men by shining a light onto the nine years leading off from Peace Walker all the way to 1984, the year the main episode of MGSV takes place.
A few facts expand on the established lore and reveal the truth about Metal Gear’s overarching narrative: Zero is already in a coma by the time Phantom Pain begins. Skull Face managed to locate him using the information he had extracted from Paz and strike at him using a deadly parasite strain. Also, while it is true Zero tried to coerce Snake into working for him again by infiltrating Paz into his organization and orchestrating an incident that could have revealed MSF’s nuclear capabilities to the word, he died a completely different man. Somewhere along the line, Zero had a change of heart and gave up trying to possess Snake as his tool; he came to respect his own friend for standing his ground and believing in something different than himself did. Which is why he went through all the trouble of securing asylum for him in Cyprus.
Not only that, but Zero longed to be reunited with his friend once more: he believed Snake and him could come to an understanding if they had a chance of talking again. Perhaps a conversation that could’ve changed the entire course of the series. But the reunion was denied by Skull Face when he put Snake in a coma during the attack on MSF in 1975 and later that decade when he killed Zero himself, dooming them to never see each other again.
The truth is that Snake and Zero were never in a true war. They had a incident in Peace Walker, but Snake knew Zero was probably not in control of Cipher anymore by the time he woke up in 1984 and that the Patriot AI’s, as reported by Ocelot, had taken control over the organization. However, he did understand what they represented: they would carry out Zero’s will and, while alive, Zero sought peace through unification. Unification being the means the major had found to achieve the worldwide peace the Boss fought for. This went against what Snake desired, so he knew that his nation of soldiers might one day fight the self-administrating organization Zero left in his wake. This, however, wasn’t certain: Snake would fight the keep the world engaged in conflict while Zero’s organization would fight to stop all wars without openly engaging with each other, similar to how America and the USSR fought the Cold War, and perhaps one of them would fall without ever engaging in open conflict with the other.
In the end, Snake understood what he was up against: an AI network designed to emulate Zero’s will, a machine incapable of changing its mind like Zero himself did before passing away, but still capable of altering its strategies to achieve its objectives - or alter its understanding of the objectives, as was shown to be the case in Guns of the Patriots. Which is why Snake accepted Zero’s gentle gesture of keeping him safe while he was under and didn’t oppose the plan of consuming the identity of his greatest apprentice in an effort to conceal himself or of sacrificing an entire hospital full of innocent people in order to evade XOF. Snake had his eyes on much bigger prizes, whatever disputes he may have had with Zero in the past were petty squabbles when compared to the scope of what he had in mind. Zero, now his phantom AI, was just one more name on the long list of people who wanted him dead, people who would serve as the forces of the times in an attempt to defeat Snake and his nation of soldiers.
Snake went to on to fight for what he believed in, as twisted and warped as his beliefs may have been. He didn’t focus solely on defeating Zero’s organization because that wasn’t the most direct avenue through which he could pursue his goals. They were clearly a force that was pulling the world in a different direction than Outer Heaven, but Snake didn't think that destroying the Patriots would necessarily make them closer to perpetuating war. In the end, however, not prioritizing the elimination of the Patriot AI’s proved to be an inefficient strategy for Snake, since it was Zero’s AI that flagged the both Snake and Venom for elimination. Sending the orders which resulted in the deployment of Solid in an attempt of sabotaging Outer Heaven operations amidst its uprising and of disabling Zanzibar offensive capabilities.
In the end, Phantom Pain alters the meaning of key events in the saga by revealing that the greatest conflict in the entire series was never truly a conflict, but a misunderstanding that grew larger and larger until the anger of one man set the fate of both man in stone. The true story is much more tragic and "meaningless" than some of the characters in previous games would make them out to be.