Might as well cross-post this and hope there's not an ancient, search-engine-evading forum post that makes a wash of this topic.
ctrl+v: "So, I went through all of Marathon: Fell’s terminals with DTB [NOTE: the only Mac we own, an eMac, can't seem to run Infinity]. I mentioned that I had suspicions about Balapoel and Parael, the scenario’s main AIs, and I don’t think that there’s anything in-story to contradict them (though I might’ve misread things).
My theory is as follows: At the start of Fell, Balapoel informs you, the Commander of the UESG Tethys, that you are a walking temporal anomaly–you were supposed to die in an accident, but some other chump bit the dust in your stead. Later on, you meet Parael, who tells the Commander that Balapoel is a former human and a criminal.
What I suspected was that Balapoel was the Commander from the 'correct' timeline, and that Parael was the guy who died in the other one (hence, when I gave them android vessels, I mirrored their insignias). Fell doesn’t seem to elaborate any further on either AI."