Perhaps the biggest problem facing the VR Theory is the presence and actions of Solid Snake in the Plant Chapter. After all, we're told that he is "not part of the simulation" by G.W., so obviously he must be real, right? And besides, how crappy would MGS2 be if Solid Snake was in our head?
But the evidence is all there to suggest that he too is imaginary. The fact that we want him to be real does not make him so—and in Raiden's case, it makes him even more suspicious. The Colonel was, after all, part of his expectations and experience, so there's no guarantee that Snake wasn't as well. Just look at the screenshot to the left, for example: Raiden is naked and trapped in a very surreal hallway, with swirling graphics and nonsensical codec calls. We become desperate for something or somebody to come by and save us; and as Raiden said before, he thinks Snake has his gear...
Eventually, it cuts to a cinema. Raiden's walking along, when we hear Snake say, "Amazing how you walk around like that." Raiden turns to see who it is... but as you can clearly see, the hallway is empty. The camera then cuts to Raiden's face, who looks surprised and says "Snake!" And in the next shot we see our hero, once again decked out in his sneaking suit, casually leaning against the same wall we just saw was empty. And as the script's notes reveal: "Snake wears the familiar bandanna on his head, which is rippling despite the absence of any breeze. This is the familiar Snake of old, beloved of fans." Wow!
Our prayers have been answered! Snake appears magically, right at our most desperate state, wearing his old suit and ready to help cover our nakedness, and he even gives us a shiny new ninja sword! He shares philosophical encouragement, spiritual direction and (ha ha?) "Infinite ammo."
Players, like Raiden, are more than ready to believe what we're seeing. The Colonel stops calling, Snake is our best friend, and we can even deflect bullets using our sword like Gray Fox from Shadow Moses! But when we soon find out that the Colonel was in our head, Raiden becomes paranoid.
Raiden: It was all -- an illusion? Everything I've done so far...?
Snake: Raiden!
Raiden: Snake -- what's happening around here?
Snake: I don't know. What I do know is that you're standing right here in front of me, not an illusion -- flesh and blood. It's your call. You can drop this if you want.
Raiden: No, I can't do that. Let's go...
Soon enough the "Colonel" calls, saying that Rose is being held in the holds...
Snake: It's a trap!
Rose: Help!
Raiden: Rose!
Snake: Raiden, get a grip!
Raiden: But Snake!
Snake: It's a trap. If the Colonel doesn't exist, there's no way he can take Rose hostage.
Raiden: Yeah -- you're right...
Snake: I am right.
It gets better after this, but the question must be asked: is Snake stupid? Even if he can somehow hear the voices in Raiden's head, his logic is absurd! The Colonel may not "exist", but somebody gave Raiden his equipment and traning; somebody gave him nanomachines and introduced him to Rose in the first place; somebody with very real and far-reaching power! ...Unless of course the whole situation is a dream, in which case logic is unnecessary. Raiden's reply is priceless:
Raiden: ...OK. But... Does Rose -- exist -- ?
Snake: Don't be weird, she's your --
Raiden: What if I've never really met her... If the Colonel is something that I partly dreamt up, then... everything I remember about her could be --
Snake: Don't jump to conclusions!
Raiden: You and Otacon are the ones who say the Colonel never existed. Is this what Olga was talking about?
For a moment, Raiden truly considers that everything and everyone is an illusion. "Is this what Olga was talking about?" Of course it is. Kojima made sure that the player would be confronted with the possibility of the VR Theory being true, even if they've tried to ignore it until now. "Snake" tries to whisk away Raiden's doubts any way he can, but he's just another illusion. His magical reappearance, "infinite ammo", and too-good-to-be-true mentoring are the manifestation of Raiden's unrealistic hopes about the legend he has come to worship.
"Not part of the simulation"? Ha! He's the key to making the simulation palatable! The simulation would never work without him! He's the one who cut the whole in the Big Shell for us to swim through in the beginning! He's been a key factor from the start. Being shunned by the "Colonel" is just another way to sell his believability to us! The ending simply reinforces this, as we will see.