So all this conspiracy theory stuff... let's count them
Merovingian (Knights Templar)
Great Architect (Freemasons)
Illumination (including a brief 23 fnord)
Obviously, all of the above have been tied together by some of the more talented conspiracy theorists out there, but what does that leave?
We've got the Men in Black stuff, obviously, but all the Area 51 stuff doesn't really apply... unless the aliens created the Matrix? However, there was that brief write-off of aliens along with werewolves and ghosts as rogue programs. Bit difficult to have Bilderbergs and the like really mattering when you're already talking to the creator (gnostic or otherwise). Anything I've missed?
So where does this go in the next part? Well, with that lot of conspiracies, they'll have to have a Grail to seek. Slightly confusingly, we've already found the messiah before the grail. What sort of grail? Maybe a standard issue magical cauldron to feed the masses, heal all hurt and revive the dead? Probably the Messiah will have to be sacrificed to save mankind, but not until Morpheus the Baptist has lost his head (Niobe seems to have a lack of children to be killed, but will she be a Salome to Morpheus' Baptist?). Skipping forward a few chapters, there's the whole Revelation chapter 21 stuff for a glorious ending.