I think that this story is deep and beautiful, but a bit difficult. You need to think about it. It's like Milton's poetry, in that respect, and if there is a metaphor in the story, that is it. Paradise Lost is an appropriate key to the story, but it isn't easy and obvious like most modern poetry. As I understand it, Milton's and the Emissary's and the Ship's conception of human value is that Story and Mission and Purpose are identified with capacity, which really is an inhuman measure of usefulness. The virus produces "diminished capacity". Emissary remembers that he has forgotten his real name, which is "his own story".
So the story is about the modern tendency to equate human worth with human capabilities rather than the name and unique story of the individual. And sending Milton back on the ship is Emissary's hope that she will be healed and get her own story, because if the Council cannot cure her, they themselves will suffer diminished capacity and death.
Innocence is having no story, so you are "Not". That has some interesting facets to it as well, since it is stories that differentiate humans from animals, and the human soul is received by the breath of God (at least in Milton's worldview), whose name is "I Am", the opposite of "Not".
(This part is my interpretation).
If you want to spend some time with this story and let it sink in, you may find yourself, as I did, wishing Jay Lake lived in your neighborhood so you could hang with him.
I don't subscribe to a lot of podcasts, so I don't know if I'm missing a world of this level of art and philosophy out there in flash fiction land. But I have listened to a few, and been disappointed I have found so little that qualifies as great. Frankly, most of it has seemed like a waste of time, which is why I haven't listened to more.
I hope Jay has listened to Clown Eggs and this story. Would love to hear his opinion of Norm's interpretation of his work.
Never judge anyone until you have biopsied their brain.
"Be kind, for everyone is fighting a hard battle."
Known Some Call Is Air Am