... OK that didn't work, so I just did opensesame...
The bug is that the levels don't save what you did previously, and are reset to exactly what they were when you came into the sub base. So, that door is locked, all items and enemies are back, and the elevator out of the submarine hangar is in the wrong place (I had to ghost up the shaft). Even worse, Jock's helicopter is just hovering above the start point instead of where it is supposed to be for the mission end, so I can't complete the objective ;_; I guess I have to start the entire level again
Also, are you supposed to give Tracer Tong his cure before you go to the sub base?