[LoweGear]

Read some spoilers for the movie, and apparently it uses one of the more common interpretations of some overarching game mechanics for the story:

Spoiler for Obvious spoilers:

They do apparently use the "Abyssals = Shipgirls = Abyssals" interpretation, in that Shipgirls sunk in battle become Abyssals, and Abyssals sunk in battle can become Shipgirls when they're rescued. And it is apparently confirmed that yes, the Abyssals are are creatures made from the anger and grief of ships sunk during the war.

So essentially, Shipgirls and Abyssals are locked in an endless battle where their casualties result in bolstering each other's forces. At least, in the anime's setting anyway.