Part 9: Product Placement
PART 10: Big Boss Returns
Page 1: A Dead Man Walking
Easily the most shocking twist in Guns of the Patriots is the return of Big Boss in the flesh, prompting outrage, excitement or simply confusion from fans worldwide. After repeatedly being confirmed as dead ever since Metal Gear 2 for the MSX2, the thought of him being alive and well by the end of MGS4 was impossible to those who followed the narrative. What possible reason could Kojima have had for bringing him back for one last farewell, and what are the ramifications?
Obvious Reasons:
Justifying the return of Big Boss is a mind numbing task, but one that Kojima nevertheless insisted on squeezing into the end of the game, which truly begs the question of "why". Putting aside story logistics for a moment, the most obvious reason for doing so was undoubtedly to give the game a surprise twist worthy of the "final game in the Solid Snake saga". With (supposedly) all of the plot holes covered by the time the credits rolled, and all of the loose ends tied up, how could Kojima surprise the players? Normally this is where we would learn some crazy secret that puts a new spin on everything we thought we knew, but since the whole game has been designed to end things, it would be counterproductive to suddenly introduce a new element that would only raises new questions; instead, the best way to surprise the player with closure would be something like this.
By dragging in and killing both Big Boss and Zero right in front of the player's eyes, there is a new level of closure, because until now their whereabouts and status have been the subject of lies and controversy, told from subjective points of view. But more importantly, it allows Big Boss to take away any doubt as to what "the truth" about him and Zero is. The man himself shows up in the flesh simply so that he can clear up the "big picture" for the player, under the guise of making his peace with Solid Snake. For those who felt that there had been no resolution of the relationship between Snake and his misunderstood father, this is key as well.
Now allow me to practice my apologetics and do my best to reconstruct how it all played out.
Big Boss was killed in Outer Heaven by Solid Snake and brought back to life thanks to Dr. Madnar's Snatcher Project in Zanzibar Land [1]. After getting killed for the second time by Snake (this time via fire), his remains are stolen by Zero, frozen with nanomachines, and then locked away in preservation using the mind control technology the B&B unit would later be given. This outrageous act unites Ocelot and EVA against Zero, driving them to hatch a "grand scheme" to kill the remaining Patriots (Para Medic and Sigint), get Big Boss' burnt remains, and finally destroy the System, which will not only reveal Zero, but awaken Big Boss* as well. To accomplish this they recruit Naomi, kill FOXHOUND with FOXDIE, fool Solidus in the Big Shell, and "fool the System" by turning Ocelot into a doppleganger of Liquid. Exactly how becoming Liquid Ocelot could possibly fool the System is unclear, but since Solidus, with both of his eyes intact sitting in the White House as President, apparently fooled Zero and the System into thinking he was Big Boss — whose remains they still had in their possession — I guess it's a not that hard a thing to do?
Meanwhile EVA calls herself Big Mama and recruits a private army to try and find Big Boss' remains, but with no luck. After the Manhatten Incident she manages to work out a deal with Raiden for the location, however, and eventually succeeds. However, Ocelot is now out of control and uncooperative†, but still secretly searching for a way to control the System using GW. Unfortunately, this results in him becoming convinced he must hunt down Big Mama and steal the remains, which he eventually does. 
Except they aren't the real remains: they're what's left of poor Solidus! The real remains have been getting repaired by Big Mama using the combined remains of Liquid and Solidus, and kept in a safe place until JD was destroyed. Once that finally happens by corrupting it with Naomi and Sunny's virus, he wakes up.
See? It all makes perfect sense! Plus it serves to tie all the loose ends of the other games together by reframing everything in a new, overshadowing context: one in which the meaning of many things we used to think were important are marginalized, and many things we thought were minor are all that matters. And, especially in this new context, it is absolutely necessary that Big Boss gets the final word, serving as perfect narrator for the long and dismal tale, having been central to so much of it from the beginning.
What Big Boss says to Snake is quite a nice commentary on life, as well as Kojima's role as a storyteller, but that analysis will be saved for another time. Instead, let's move on to the possible problems and hidden reasons for what Big Boss' return means, so that we can gain a fuller appreciation for why it was included...
PART 10, pg.2 NEXT
* Big Boss: That body Liquid burned on the Volta... Wasn't mine. That was the body... Of a clone. Solidus. He was a perfect clone. Zero, and the proxy AIs that came after him, were convinced that Solidus was me. I was implanted with nanomachines... Kept in a state of eternal sleep... By JD the proxy AI. They had me sealed away completely... Not only physical body, but my will, too. The technology was similar to what they used to restrain the B&B members you encountered. For me to wake again... The System had to be destroyed... One way or another. Ocelot and EVA wanted two things... To bring me back to life, and to end the Patriots. That meant destroying the AI and killing the man... JD and Zero. Right before you uploaded the virus into GW... The way to JD was opened, but only through the physical manifestation of GW. That's when we finally learned the location of this man... Zero. For me, and for them... For Naomi... Nothing was more important. And it was for that they put their grand scheme into motion. EVA stole my body from them and reconstructed it by replacing the missing parts with pieces from Liquid and Solidus. And Ocelot... In order to fool the System...
† Big Mama: Naturally, Ocelot and I planned to free him from Zero's prison. We enlisted Naomi Hunter, an authority in the field of nanomachine research, into our organization. And we used Frank Jaeger to kill Dr. Clark. Ocelot tortured the DARPA Chief, Donald Anderson - also known as Sigint - to death... And made it look like an accident.
Snake: The Shadow Moses Incident....
Big Mama: With Para-Medic and Sigint dead, Zero was the only one left. But we, too, paid a price. I lost Ocelot. Ocelot wasn't fighting for the Pentagon, or the Russians. And certainly not for Zero. He was fighting for Big Boss. He idolized him. When Ocelot grafted Liquid's right arm to his own... His body was taken over by Liquid's thoughts and spirit. He may be Ocelot in physical form, but his mind is Liquid's. I was the last one.
