I had given notice I would return when ready, and so I have. Here, below, is as much as I can do to create a clear map of the choices that underline the timeline. To make my purpose clearer, I wish to de-tangle the web that is Moo into a coherent stream of choice and consequence. I submit it to you, sirs, for those with a clear eye to fault my human erring.
Previous mappings of the different possibilities that are presented in M2 and Moo made frequent reference to the concepts of 'success' and 'failure', as these are the grounds for the player's frequent reality-hops. However, for my purposes I care not for these concepts, moreover they would present an interference in what I strive to achieve. The below is a mere dissection of cause and effect.
Initial Choice: Stay with Leela[1] or go with Durandal[2]. Presumably made in Ingue Ferroque.
[1]
Choice One: Presumably, there is some decision that helps or hinders Durandal with regards to locating Thoth. The possibility that the same events that determine the differences in the 'Durandal timeline' is one that excites me, though I believe there is no direct indication of what this event might have been within any formal Marathon canon and therefore it lies within the realm of pure conjecture.
If Durandal is helped, then he discovers the Sph't in time for them to balance out the battle, and presumably they interfere with Durandal's destruction, and thus are at cross with Tycho and the player's purposes.
If he does not, Durandal is assaulted and boarded, much as he is in M2, only this time the player is not there to curb the invasion, instead helping it on. It is possible to conjecture that either way the player makes little difference, here.
Choice Two: A personal choice, for once, of the player to take Durandal's primal pattern. Most probably because Tycho does not see the player as an immediate threat, they are allowed to do this unmolested until the retrieval and safe storage of Durandal. The rest follows as we know: The player is temporarily conscripted into Tfear's service, then escapes to merge Durandal and Thoth.
If the player does not... there is a question, indeed. What would have occurred had the player not taken the primal pattern, or not been in a position to do so? The Sph't'Kr would have not arrived, and neither would the trith xeem been forced into usage. From a universal point of view, a satisfactory outcome? Not within my immediate purview, perhaps, but important I feel nonetheless.
[2]
Choice One: Presumably, something occurs between leaving Tau Ceti and reaching Lh'owon that leads Durandal to have a much better idea about the location of Thoth, leading to the AI's much earlier activation. Also, a Pfhor commander decides to follow Durandal, leading him to wake you much earlier than before in the chronology of M2 events. However, the AI is unusable and Durandal is beset by the Western Arm much earlier than before.
If Durandal does not gain this information and the commander does not follow him (I am inclined to believe that these events are linked), then M2 proceeds as we have experienced it.
No further decisions can be made here, actions have lead to a unavoidable course with disaster, disassembly and nothingness.
Again, I humbly submit this to you that your noted knowledge and wit in these areas may come to some use to us all, no more. I would rather response than, for some example, jests about a certain Mr. Cruise. Certainly, you know exactly who you are of whom I speak. :P