“Ghost Babel and the Acid games were created in something we call the "parallel universe" of MGS. This gives directors like Shinta Nojiri more freedom in creating exciting scenarios for Snake to overcome. I'm toying with the idea of doing Metal Gear Saga Vol. 2, featuring the games from the parallel universe. I even joke around the office that I'll name it Nojiri Saga Vol. 1. “
- Ryan Payton (1)
“Parallel universe? WTF!!!?!! That’s never mentioned in the official games.” Well, yes, they are. It seems widely accepted that Ghost Babel and the AC!D games take place in a parallel timeline to that of the main games. Look at the Snake Tales in MGS2 and play External Gazer. While this may be a ploy by Kojima to get us to think about the nature of video games, it also establishes the existence of parallel universes. Dr Koppelthorn’s VR machines not only punch through to different dimensions, but also allow the person undergoing VR training to control another person in one of those separate universes.
While many would rather ignore Snake’s Revenge, it IS a Metal Gear game. What to do with this oddity? By way of torturous mental contortions, some try to squeeze it into the main timeline. This does not work for a variety of reasons. Instead, it fits rather nicely in the alternate timeline, in between the first Metal Gear game and Ghost Babel.
The same controversy over where to place MGGB is similarly resolved. Now, some have even said that this is a VR mission that Raiden goes through. Those people have not been paying attention. Firstly, it is at the end of the VR missions in the game that the dialogue between No. 4 and “Jack” occurs (see The Snake Soup's article on this (2)).
Secondly, Raiden (if that is indeed who Jack is: it could be Big Boss for all we know) is told his skills surpass those of Solid Snake at the time of the fall of Galuade … meaning that the Galuade mission happened in the first place. This would contradict all the events in Metal Gear Solid ... again, see The Snake Soup for details (3).
So all of this means that an alternate timeline can be created as follows:
MGS 3 > MGSPO > MG > MGSR > MGGB > MGA > MGA2
The official timeline goes something like this:
MGS3 > MGSPO > MG > MGSS > MGS > MGS2 > MGS4
While the latter timeline is pretty much set in stone (although you could chuck the audio dramas in there too), the other timeline is a matter of interpretation (which, I suspect, is half of the joke with regard to External Gazer). Indeed, you could include the Snake Tales missions as further branches off of the main timeline after MGS2. And just what is the real ending of MGS: Meryl or Otacon …?
The timeline on this site starts from Metal Gear, the events prior to which are the same as the official timeline. However, if the sections on the AC!D games seem somewhat indepth, that's because they're far more convoluted than the other games. See the Wiki entry for MGA2 for details of the overall plot (4).
So, if the Patriots seem absent in the alternate chronology, who is running the show? There seems to be a conspiracy between various governments and corporations to make sure a certain series of events (usually wars) occur, so that they can make money and increase power. Sounds familar? It is a similar situation to what we know of MGS4, where there is war without end ...
Final thought: if there are connections between different dimensions, caused by VR simulations, who is to say that THIS is not the real timeline and the one with MGS, MGS2 and MGS4 is just a random thought experiment dreamt up by Mei Ling ...?
(2) Snake Soup article on MGGB as a VR mission (or not!)
(3) Snake Soup article on MGGB as a part of the main MG timeline (or not!)
(4) Metal Gear Acid 2 Wikipedia entry