As much as I hate to say this, perhaps it's something like the system used in Halo. In the first game, Cortana resides on a fairly small physical neural net. While this system provides the hardware of sentience (for lack of a better way to phrase that), it fails to grant her enough processing power to actually operate; she requires the thing to be linked to external processors before she can sustain her consciousness.
Reference is also made to a process by which some AIs "think themselves to death." AIs in Halo fall into two categories, those whose thought processes are unrestricted, making connections throughout their neural nets untill they have depleted their resources; and those whose thought processes are limited, who are spared this ultimate fate. Compare this first form to a rampant AI, it's thought-controll systems shattered, growing rapidly, requiring ever greater resources, eventually depleting them. Compare the second state to a pre-rampancy AI, it's thoughts restricted, likely to the immediate end of allowing human controll over them, but also preventing them from gorwing in such a manner that their resources are consumed.
while that is Halo, not Marathon, the paralleles are (to my mind) somewhat Striking, and we know how many other ideas Bungie re-used, even if there is no explicit connection.
This theory can, to some degree, be developed entirely from the information we are given in Marathon. Durandal's pattern, the thing he transmits around and jams into your impenetrable brain-pan, might be a representation of the state of a neural net, an image of the connections that constitute his soul, baisically. This is what he transfers to the Pfhor scout-ship (presuming he located a sufficiently large neural net on that vessal that he could appropriate), and this is what he jams into your skull.
As for the odd ability of the Compilers to interface with the Marathon's AIs, or for that matter, Durandal's ability to execute on Pfhor and S'pht platforms, Leela's ability to run on Vylae hardware, and Tycho's ability of operate on Pfhorsh systems, has anyone considered that all three architectures might ultimately derive from Jjarro systems?
We know, or at least we strongly suspect, that the player uses barely-comprehended Jjarro technologies. The Pfhor scavenged their advanced systems from the Jjarro. The S'pht were clients of the Jjarro, arguably created by the Jjarro. It is at least possible that the player is not the only or even the first purpose to which the Jjarro's arcana where bent. If all three architectures - at least as far as the neural nets, the sapient parts, are concerned - ultimately derived from the same technology, it actually some manner of sense that at least limited interaction would be possible.
I should appologize for how barely-lucid and error-laden that is. At the moment, I feel something like I'm being attacked by the S'pht. If I can pull myself together a little bit, I might try to salvage something sensible from that.
