I've mentioned here before that in the past couple years I've seriously revised my thoughts on time travel and especially its implications on the plot of Eternal, and have since come up with a couples ideas for what I would have done, had I the opportunity to do it all over again from the state. My favorite of those ideas involves this whole Jjaro at Tau Ceti thing, and I thought just now that maybe I should share it, in case any aspiring scenariowrights or fanfictors out there should find it nifty and want to make something of it.
The idea was sort of to do for M1 what Infinity did for M2. It would take place in the aftermath of Marathon 1, in an alternate timeline where Marcus (the player-character) stayed behind instead of going with Durandal. Along with the other Mark IV cyborgs on the colony (amongst them the one who would eventually become Hathor), he would try to fight back the Pfhor when they returned to Tau Ceti. In the process of this, a mysterious Jjaro artifact would be uncovered (hinting at the very old version of Marathon's plot which featured you as an electrician investigating a strange electrical anomaly discovered on the surface of Tau Ceti IV), having been detected and investigated by the Pfhor (who seek to destroy all Jjaro technology they come across as per M2). Eventually the Pfhor would end up nuking Tau Ceti down to bedrock, as per M2; but this time Marcus would have been killed with them.
Snap back to the beginning of all these events, ala Infinity. That was teh fail, try again. Several timelines along these lines would elapse, the details of which I've never worked out, but all of them involving attempts to save Tau Ceti from the Pfhor; some of them involving returning to the Marathon, some of them involving boarding Pfhor ships (and perhaps being captured, maybe leading to the "Despair" chapter of Infinity), etc. But one way or another, you would always fail to save Tau Ceti from the Pfhor. In the end, the best you can do is manage to escape, and leave with Durandal instead, with the events of M2 following. I never worked out how you could choose whether or not to go with Durandal, nor the nature of the Jjaro artifact (other than that its discovery prompts the Pfhor to nuke Tau Ceti and also saves you by sending you back in time, ala uncovering Thoth in Infinity).
I did want a major element of it to be Marcus and Hathor acting as leaders of the other cyborgs, her having been their leader during the first Pfhor invasion and you being an impressive outsider (having single handedly saved the Marathon) who she detaches some of her squad members to. You and she would run separate missions, each accompanied by four other cyborgs, and communicate with each other via terminals. From her you would get the impression that you're not the only one experiencing these events over and over again, and in the dreams between timelines you would dream together... of your past encounters on Icarus and Thermopylae, and perhaps of other lives more distantly remembered; or lives yet to be lived. The decision to abandon her and the defence of Tau Ceti to save your own ass (and the future) would thus be a major heartbreak/betrayal.
If anybody is interested in taking up a project like this I'll happily flesh the story out some more, and put together some nice landscape textures for the surface of Tau Ceti IV and such (I've already got a nice one for the space above Tau Ceti)... combined with the weapons/monsters/textures/etc from M1A1 you've got everything but the maps there. I'm not really up for leading another project, even with Eternal about to be completed; but I figured I thought I'd throw this idea out there anyway, for posterity, what might have been, if nothing else.
Also, if the name wasn't already taken, I think I'd call this project Tantalus. Which gets me wondering what the plotline of Operation Tantalus was anyway... IIRC it was the first nonlinear scenario ever, and was for M1, and I think Hamish was involved in it? It'd been a damn long time. Anybody remember that scenario? Ah yes... here it is.