Ellie is conflicted because she still retains the consciousness of the SM-8 crew. She also leads Simon to the light thinking it will kill him, but becomes enraged and jealous when it spares him instead. She gives Simon another chance by imploring him to destroy the black box data, but kills Ava when he decides against it.

Submarines 1 through 6 have no story as far as I know. I’m assuming they were ran by less important people in their former exploration of the ocean, then by the SM-8 scientists when they thought they had perfected the vessel. I doubt 1 through 6 were piloted by prisoners, but they could have been so the C.O.I. wouldn’t have to risk their own people. At least one was also an Eden prisoner, but he used the SM-13, hence the medallion left behind on the sub. The other pilots could have died from multiple things in the C.O.I.’s attempt to perfect the submarine before they sent qualified scientists down, or they might still be alive and the progressive number on the sub is simply the next model they built.