I don’t know if I missed any instructions or something but I was really tired when playing this section and was having a hard time staying awake. After clearing the tunnel of the biomass that looks like the creature from the game Carrion, I spent like 20 mins running around the pump room with no idea what to do. If you are stuck at this point like I was, you have to use the launch ability to pick up the yellow crates with the slowly pulsing lights and throw them into the the matching glowing lights on each of the 3 blue pumps.