Shay and Vella Finale
This trophy is missable. First, you need to control Vella. Leave the Control Room and enter the Fake Control Room. Use the Death Ray Remote to trigger the Death Ray. As Alex's Ship overheats, he will disable the circuits in the Circuit Room.
Switch to Shay. He needs to talk to Alex, but Alex may not have returned from the Circuit Room. Go through the door that was used by Alex and climb down the ladder. Climb back up the ladder and Alex will be back in the Ship's Control Room. Talk to Alex and there will be a dialogue option where he states that Vella possibly deliberately turned on the Death Ray. This is the dialogue that you need to hear to earn the trophy.