Parallel Universe
VR missions have been completed, Snake wakes up in a chair hooked up to a computer…

“I was sitting in the VR training seat.”
From here, Otacon explains that the VR hookup directly controls signals to the brain, and is thus “completely indistinguishable from the real world, down to lights, sounds, even your sense of smell and touch.” It gets weirder from here. Snake says it feels like he’s possessing somebody else…

“I feel like I’m possessing someone else’s body.”
Mei Ling’s appearance and the subsequent banter revolves around this, an article in the local newspaper about the giant monster at Big Shell. The two of them gang up on Snake, pressuring him to go capture the monster so they can build a zoo and sell tickets, because Philanthropy is broke. Snake tries to argue, but they keep interrupting and force him to go check it out.
So the phenomenon is real, and Snake has photographic proof. Olga — or a woman who physically looks like Olga — appears on the Big Shell and ends up confronting Snake, saying that the monster is the key to returning to her own universe, and that they should monitor the activity using the VR device Otacon made. Bad guys shows up, Snake kills them.
From a game design perspective, all this is an extremely contrived setup to discuss some very interesting situations, which may or may not have embedded messages for players to think about! These include:
- The existence of infinite parallel universes (tip: for further research)
- VR simulations being disruptive visits to these parallel universes due to the mysterious power of the Kopplethorn Engine
- The Gurlugon being the “singularity” fulcrum around which space-time corruption occurred
- Mei Ling suggesting to kill the Gurlugon
Thus, by tracking anomalies through the VR system and detecting the presence of Gurlugon, they track him down. Snake fights him in the hopes of restoring reality.
Does reality turn back to normal? Of course not. From here the story becomes even more absurd, as Mei Ling is revealed to be an evil doppleganger who is married to an inter-dimensional Solidus, who blows through the wall and escapes with Mei Ling before they can stop him. Otacon and Snake hatch a plan to search for the “Olga” they met earlier by putting an ad in the newspaper. With a wink and a nudge, we meet a doppleganger of Fortune who’s really happy:

“Good luck?! Is that a skill?”
Over and over, we see a level of self-awareness that drinks in player criticisms instead of giving us what we want. It’s all in good fun, of course, but as the story progresses things become even more deranged. “Olga” tells Snake and Otacon to search through parallel universes (“VR missions”) in order to track down other singularities, with the hopes of capturing one. Therefore, back into VR we go!