I’m sure there’ll be references to some mysterious explosion in the Milky Way, but yeah, I can’t imagine them really addressing much of anything from ME3 - that storyline’s over, and they’re clearly trying to set up something completely different for this arc.

Most likely by tapdancing around the issue entirely. From a narrative standpoint, you establish that the ship was launched before the conflict of ME3 was decided, probably as some sort of insurance policy in case the organics lost. Then you establish that because of the vast distances involved, communication is…