The entire game is meta commentary using the players to show developers how people react to having their expectations pulled out from under them
Read the following in AI Campbell's voice
You thought you knew what kind of game you were playing? Don't be a fool. We removed Kojima from the company directly before the game launched to stir up doubt within your heart. Yet you still pushed onward, ever faithful that the game you expected - the game you were promised - would come to be. Once the time came for you to experience the game for yourself, you were greeted with a two hour long guided tutorial, in order to make you comfortable again. But this, too, was false. Over the next sixty hours you witnessed only five hours of story, story spread out so sparingly and erratically that you could not help but hope there would always be more. Just when you'd reached the height of your hopes and expectations, we deliberately inserted the song you love into the most mundane cutscene in the game. Then, seeing your reaction to Skull Face's anticlimactic death, and your absolute thirst for more, we knew the plan was successful. We initiated... phase two. We again played with your expectations by showing you a trailer for chapter two, which was used in exactly the same manner as your briefing for the mission. That's right - you were set up to fall in the same manner as you were for "Chapter 1", and you took the bait, despite over thirty hours of your time having just been spent proving that your hope was fruitless. To put salt on the wound, we took away the only facsimile of a conclusion that the game had, replacing it with a last minute twist to further throw you off guard. Eli ran off with Mantis, never to be seen again. Now, here's where it gets interesting. You passed the first two phases with such flying colors that we initiated a phase three. We put the scene on the collector's disc, knowing it would spread to Youtube. Despite your direct first hand experience with betrayal again and again, you predictably began to doubt what you'd seen and hoped that there was an explanation for the phantom pain you felt upon completing the game. No, that was all part of the plan. At the height of your denial, your absolute refusal to accept that your expectations differed so greatly from reality, we released the Chapter 3 title card on the web, followed shortly thereafter by a "hidden nuke cutscene" you could never possibly achieve.
You are the perfect pawn. You have played into our hands swimmingly at every turn. You have proven that society consists of sheep who cannot think for themselves, who will deny the truth in favor of what they want and expect from life. We cannot allow this to happen. We, The Patriots, must wrest total control from the industry. You've been an excellent pawn... "Big Boss."
We've all been fiddled
