Metal Gear Solid showed that when given the chance, the powers that be will prefer to keep you as a pawn until you outstrip your usefulness. It was a story where the main character found himself manipulated by all sides, fighting for no cause whatsoever, and he ultimately reached the other side a liberated man.
So, Metal Gear Solid 2 starts us with a man being blatantly manipulated from all sides, who is sick of the vagueness of his orders from the very early phases of the mission, and only receives orders that parrot the people he was told "Aren't part of the simulation" or ones that feel a little two NWO for Jack's tastes.
The ultimate reveal of Metal Gear Solid 2 is not that you were being manipulated again- that much is obvious. Everyone in the story acknowledges it, and it's never raised as a point against Jack. The reveal is that the antagonists were being manipulated as well, and the true antagonists were never there in the first place.
The elusive Patriots, controlling all aspects of the mission and dictating how the mission will go through various men on the inside are just a phantom. The post-credits codec call isn't a hook, it's the answer. The Patriots were dead, what is left is what they passed on, their memetic legacy that formed in the White House since its inception. All they are is a series of AIs that send out orders, ensuring an automated system of constant control is maintained, but the cracks are even starting to show here.
In the final confrontation between Jack and Solidus, a confrontation of two men molded by the Patriots AI (as a point of contrast to the "embarrassment from the 70s" that were Solid and Liquid), the AI is almost desperate in its attempts to appeal to Jack's pathos. Reminding him of Rose, who it has also tried to convince him is fake, destroying his life and trying to build it back up with ideas of saving Olga's child, they create a complete mess of Jack's mind in a way similar to what the player will feel when watching their 15 minute long spiel of contradictory information repeated ad nauseum.
Jack throwing his identity away at the end is a sign of throwing away that control that the Patriots had. He was molded by artificial values and made to feel ashamed of a past he never tries to remember, so his solution is to walk a different path from Snake. While Snake took his experiences and went on to form Philanthropy, an attempt to find meaning for himself, Jack throws away those experiences and personality. Upon meeting with Rose in the finale, his actions aren't to dodge her romantic pursuits like in the codec calls throughout the game, but to instead confront the looming issue of marriage, and how his former self, how "Raiden", could never imagine that idea.
The conclusion of the game is only the tip though. A lot of the ideas I mentioned are the base text, told to you by the characters or the Patriots AI. A few things to clear up would be that everything that happened was real though. There was no VR simulation, we just see a cleanup crew pop in to assess Arsenal's damage to New York while people go on with their day. It's cheap, but that's because the original ending was scrapped late into development due to the incident that happened earlier in the year.
To move on from that though, the game raises some interesting ideas. The parallels to MGS1 are this very clear surface level text, but the point of the game is not to show us the similarities, but instead for the player to notice the differences. Shadow Moses was an isolated island, a piece of land created by nature, with a facility that nature is constantly reclaiming through the snow or that forces the player to wander through nature's hallways, caves. Compare to the Plant, a completely man made "island", one that is almost entirely this sterile orange colour, an "island" where you'll never encounter rain or snow, let alone vegetation growing out of the floor. Where Metal Gear Solid was the "Gene", the natural idea of passing the torch, 2 is the "Meme", the uniquely human way of passing it down, and this contrast is shown in the environments.
How about the mysterious ninja? In the original Japanese, he uses Grey Fox voice clips instead of just Olga's voice through a modifier, using a "Meme" of the Deepthroat of Shadow Moses. The opening of Metal Gear Solid 2, the self-indulgent Tanker chapter, also cashes in on this meme idea. Lines from the first game will repeat themselves, Ocelot repeating Liquid regarding how much he cares for Russia, and Ocelot (fully as Liquid) repeats a line from Grey Fox, "You haven't aged well?"
Nuances like these, which add to a full reading of the duology that is Metal Gear Solid 1 and 2 are lost with a dub only localization, that also has two different translators (and a second one that is significantly less likely to be fluent). Metal Gear Solid 2 actively preys on familiarity with 1, expecting the average player to immediately catch onto what's going on, before pulling the rug out from under them with the game itself breaking down under the tremendous weight of recreating Shadow Moses.
To end another rather rambly series of notes, I'd like to highlight the 3 novellas you receive in the game, which convey the information age ideas of the title. You essentially read an interpretation of an interpretation of an interpretation, to unlock an interpretation of an interpretation. Even the original file itself is just Nastasha interpreting (sick of this word yet?) the events of Shadow Moses and her relationship with Richard Ames, and this document highlights how flimsy loyalty to the Patriots really is for a lot of these people.
At the end of the game, I found myself seeing the Patriots as a washed up group, desperately clinging to some semblance of control that they were losing as the game kept going. Everyone in their employ appears to be there unwillingly or due to their own lack of knowledge, and the sole committed member, Revolver Ocelot, has been compromised. It's a rather optimistic note to end on, that these people controlling society can't wrestle their hands around the throat of an information age much longer. They've resorted to their own subjects, trying to influence them to filter the information and only accept the Patriot approved truths, but Snake gives Raiden the words needed to see past that.
"Find the meaning behind the words, then decide."
Oddly, this game doesn't follow on from 1's anti-nuke critique with a similar series of endcards. Perhaps the information age itself is the "nuke" of this new and unfolding world, and we should be wary of the consequences of letting people decide what information is important for us.