Colorful, Sweet and Just a Bit Scattered

BloodyMary Atlantis: The Lost Empire AU (with a twist!)

Grace is obviously our Milo Thatch, a passionate scholar discounted for his radical theories and recruited for a mission that may actually prove them right. The expedition party consists of the Hail Mary team and the COI, pursuing knowledge and resources respectively.

They reach Atlantis and find a living human civilization whose people believe the world above was destroyed centuries ago and only their ancestors were spared by the mercy of some deity they call The Last Tree. Their leader, the Father, assigns a handful of his faithful the task of "guiding" these visitors during their time in the city - or, more accurately, keeping them in check and finding out what they know. Despite warnings not to trust the outsiders, Simon quickly becomes fascinated with this overworld they claim to come from (and with Grace but that's beside the point) 

Loyalties are tested, secrets are uncovered, powers emerge to threaten both worlds, and the unlikely duo find themselves caught in the middle of it all (dun dun duuuuuun!)

I'm just debating whether to make Rocky a human member of the expedition or have the Eridians as an endemic species pre-dating Atlantis, because I refuse to leave out Grace's bestie!

Simon doesn't call the Hail Mary by its name, only ever referring to it as "the ship" and never addressing its AI directly. After learning about Eden and the SM-13, Grace initially attributes this to a mix of religious trauma and associating the disembodied computer voice with the speaker on the sub.