I've been replaying the series for the first time in probably a decade and while I grasp what MGS2's story is getting at I'm hoping someone can clear up a plot point for me.
So The Patriots (who are now essentially the AI constructs Zero desired to succeed him) concoct a plan (S3) to test their latest AI system, GW, by manipulating Solidus into a terrorist act aboard the Big Shell (which is just a cover for the final stages of development of GW and the Arsenal project). Ok cool so far.
They send in Raiden to see if GW can manipulate him into doing their bidding by selectively feeding and denying him info as well as faking scenarios and contacts (the Colonel) throughout therefore testing GW's capability of doing the same with digital info on a global scale.
Why then does the GW AI itself allow Raiden to gather Emma Emmerich and her digital Foxdie worm cluster and use it to effectively destroy GW (itself!)? It makes no sense. The protection of the Wise mans Committee's identity is moot as it's an "half truth" (like what you did there Kojima!). It never really needed the cluster to vector the deletion of that information as it was another misdirection.
The secondary AI mentions (prior to the final Solidus/Raiden battle) something about completing GW with the inclusion of the worm cluster, but that can't be as, as of MGS4 GW is in ruin and is the very thing re-purposed by Ocelot to finally bring down the AI constructs.
It's seems that the entire purpose of the S3 plan to test GW was pointless as the other AIs essentially destroyed the very system they were testing/supplying test data to.
Tested what the AIs can ultimately do, but destroyed GW so Solidus, or anyone else, can't take advantage of it. It mostly took down the Patriot's data from it, and negated Solidus' control over Arsenal and the military AI. It was the AI's ultimate way of saying "you can't touch me" to everyone in the story.
I honestly think that the MGS story was going a totally different way from what we got in MGS4, GOTP retconed the master story that MGS2 (and even 3) was.
I mean, The Patriots were such a mythical entity, but then MGS4 went and said "uhhhhh do you remember the comedic relief of MGS3? uhhh yeah yeah, well, THEY are the Patriots"