[@Burning Kitty] Well, I don't know how that would fit in your plot but maybe they could be discovered? The Quarians maybe having their back on a zone with Remnant structures with defenses that attack anything that gets too close and a voice giving what people can only assume are warnings to get out. When the pathfinders encounter the Quarians and are told that it makes them curious, especially since remnants never, ever bothered to say something before. Cue the Composer telling the intruders once again to leave this place but the newcommers proceeding, fighting some remnants as Composer sends what he has at them until they go deep enough in the complex and the Composer awakes the Conservator to try and defend the site. Cue a nice little chat after that.

Or maybe the Quarian Pathfinder went through all of that already and the Jardaans are awake.

Also, who's the Initiative's Ambassador? Ye know, the person Ryder places in charge after the game until elections become feasable.