Possible Story Ideas

[Neoteny]

Remember also that Zion and Carlyne used a specific code to prevent Halborn from reaching the Matrix - this could obviously be researched, adapted, and applied to the multitudes of Oligarchs as well, given time and data.

Also remember Helian and Tesarova came back using enhanced methods of accessing The Matrix. If it came down to a coding battle, I'm fairly sure the civilisation capable of downloading their minds into synthetic android bodies would win everytime.

I don't agree. Just because they have their abilities and codes (which, again, have been largely cancelled by Cryptos's efforts) doesn't mean that others couldn't out-code them, especially when said others have more knowledge of and experience in the Matrix. I guess it all boils down to the argument of "how advanced are they really?" I mean, if they were so great, they could've created the BIP themselves, couldn't they? Obviously the Machines and the Programs have something on them.

Moreover, I don't see wiping out the Oligarchs as necessary. What I do see as necessary is fleshing them out. The reason they were so goddamn boring is that for months at a time, we would just see them somewhere attacking worthless things or wandering around without any explanation. Make them get involved more (somewhat like Helian and Tessarova). Integrate them into the story rather than destroy them. Or, if they must be destroyed, have it be the result of a conflict in the Real between the Machines and the Oligarchs. But put them to use and get people interested in them. Don't just have them fade in and out.

In any case, I still don't see motivation for the BIP to destroy the Oligarchs, so I really think that if they're to be removed, it could be done via:

a) Merovingian/Machine collaboration (including research of Beirn's cheat code powers in conjunciton with Cryptos's code which could lead to pushing the Oligarchs out)
b) Machines harnessing some of Sati's programming in conjunction with the programs they have to push the Oligarchs out/render them powerless.
c) Machine/Oligarch war (which seems like the eventual resultant of the Oligarchs being kicked out of the Matrix anyway)
d) Machines kidnapping BIP and using it to do the whole golden hallways reset thing which somehow magically kills oligarchs/blocks them from the Matrix (my least favorite option, since, if you look at it, contains no real further explanation as to why or how the BIP accomplishes this, since it's just code as much as anything else, and that a server reset wouldn't seem to do much...)

I'm sure there are other options to remove the Oligarchs, they just need thought. But again, I don't think removing them is entirely necessary. Just strip them of their power or kick them out of the Matrix and you're essentially golden - not killing off characters in a villain of the week type of action and retaining individuals who could be used to further plot either immediately or soon thereafter.