Part 10, page 1: A Dead Man Walking
PART 10: Big Boss Returns
Page 2: A Wrench in the Metal Gears
Hidden Reasons:
Let's drop the apologetics and get real here for a second: Big Boss coming back at the end of Metal Gear Solid 4 is pretty much a big steamy dump on the freshly molested body of the series — storywise, at least. We've just witnessed some of the most grotesque absurdities and stupid retcons imaginable, and now when Solid Snake is going to end it with a fitting "bang", he pussies out and realizes that Big Boss was creepily watching his suicide attempt from the sideline. What he is about to say will soon make us regret him not pulling the trigger.
For those who have no qualms about how the characters in the series are handled, this is just a strange occurrence on par with a lot of other crazy things that have already happened; but for those who hold the plots of the old games sacred, this is truly blasphemous. And yet... that's sort of the 
point. Why do you suppose Big Boss is openly compared to a religious Messiah throughout the game? His life and death are considered untouchable in the eyes of the hardcore fans, and even if you didn't think so before you started the game, you should by the end. The cathedral scene makes it obvious enough, but once you combine this with the ongoing theme of an "Outer Heaven" and the coveting of his remains, you start to get the picture. Big Boss is very dead, and very important.
If Big Boss is supposed to have overtones of a Messiah, then the graveyard scene is both his Ressurrection and Second Coming at the same time; an event that was prophecied by nobody but perhaps the most loony of fans, and which heralds nothing but an unnecessary wrench in the gears of the plot. In the end he more or less admits that everything in the series was really stupid once you think about it, and pretty much apologizes for not just "letting the world be". His words to Snake are Kojima's to the player:
Big Boss: It's over. Time for you to put aside the gun... And live. It all began with a bunch of old fools. Now... They've all passed away. Their era of folly is over. I'm the only one left, and soon... I'll be gone, too.
If MGS4's series-wide retcons are to be taken seriously, it was all one big era of folly indeed; one that Big Boss was the highlight of. I mean really, he's a Frankenstein's monster, cobbled together from his murdered clones and brought back for no better reason than to turn off the life support of a senile geezer and die. This is what it was all about? This is what so many tens of thousands of people were killed for? This is the big secret that Snake was being kept in the dark from? Talk about unsatisfying.
SnakeSoup did an excellent Myth article on why Big Boss couldn't be a Snatcher back in 2004, but thanks to the MGS4 Database he had to completely go back on it, despite the evidence being stacked in his favor. Kojima is so eager to destroy the integrity of the character that he even resorted to needlessly indulging the stupidity of the much-despised Snake's Revenge, in which Big Boss is revealed to be a cyborg. Kojima apparently mocked this in Metal Gear 2 when Kessler mentioned a 
rumour that Big Boss had been revived by the Snatcher project, much like how Solid Snake says he's "not a fan of blades" in Metal Gear Solid 2. Except, in MGS4 he's using a knife the whole time... So I guess Snake's Revenge gets the final laugh yet again.
Don't let these things slip past you. If Kojima was vigilant enough to mock Snake's Revenge in subtle ways in two games that came after, purposely contradicting both of those mockeries now is certainly worth raising an eyebrow or two over.
What, then, is the motivation to confound the series with Big Boss' return? Why throw a wrench into the gears? As with Vamp's sudden change into a work of science, Big Boss' return forces the player to choose between the old series and MGS4. It forces those who were demanding answers to make a hard decision between rejecting the now-canon rubbish explanation for things, or staying true to the old games and figuring out things for themselves. I know I would rather forget the "answers" provided by MGS4 and draw my own conclusions about what happened after MGS2, and I think that was the point. Big Boss is here to throw a wrench into things we loved, to provoke us into finally giving up on knowing every stupid detail of the universe, and instead recognize the "important things", or SENSE, of the series.
