The story works in a few time frames. First, there is the present moment, where Bishop, a "troph" (a humanoid creature) is investigating the crashed ship of her comrade, Jones. Jones' ship has been pinned to the ground by a UFO. There is also the near past, where Bishop is training in the Tank, a simulation machine which prepares her to deal with real-world combat scenarios (the Trenches.) Then, there is the far past, where Bishop is a refugee on a ship also named Bishop. It is implied that when Bishop was "saved" by whomever saved her and the other refugees, she became a sort of super-soldier for them. (This part was unclear and hard to follow; hinted at rather than told.) Bishop and a few other trophs go onto Jones' ship to investigate it. There are no signs of life on either ship. They go to the infirmary, which is covered in liquid methane. Jones' body -- or what remains of it -- is buried beneath this methane, just a black mass of smoky material. Then, the story flashes into another perspective, that of Baroness, a collective creature that has somehow melded with the alien ship (the Vispin) and enters Bishop's consciousness. The story ends with Bishop piloting her and Baroness out of the planet's atmosphere.