The Ophelia Prophecy by Sharon Lynn Fisher

Asha and Pax, strangers and enemies, find themselves stranded together on the border of the last human city, neither with a memory of how they got there. Asha is an archivist working to preserve humanity’s most valuable resource, information – viewed as the only means of resurrecting their society. Pax is Manti, his Scarab ship a menacing presence in the skies over Sanctuary, keeping the last dregs of humanity in check. Neither of them is really what they seem, and what humanity believes about the Manti is a lie.