: It's possible that the intended story is as straightforward as it sounds,
: that it's just that the Covenant AI was familiar because it was based off
: of a human AI because the Covenant are imitative not innovative (or based
: on Forerunner stuff she was already familiar with), but I like this idea,
: as it brings so much more complexity to the world and plays with time
: travel in interesting ways. I wish it was the intended story, even though
: it very well may not have been.

We can't know for certain, unless Nylund or Catalog say so. But what pushes it to me from "seems possible" to "likely intentional" is when Cortana is examining the AI and finds "small portions of the alien software looked like her. It was almost as if it were her code... only copied many times, each time with subtle errors introduced by the replication process. (p.237, 2010 edition)" She also mentions that there'd be no reason for the Covenant to copy an AI over and over because each would inherit the shortened lifespan, and the Justice AI itself seemingly confirms it's been copied because when being killed it yells: "I go to finally to my heaven reward paradise final-final-final-infinity-infinity-infini-AT NONCOPYSTATE. (p.209)" So who knows. But there were a lot more seemingly direct clues than I expected to find.