Queen of the Deep — Philip Jose Farmer

Jones was on his way on a Luxury Liner when it was suddenly blown up. He is captured by a robotic enemy submarine. The secret high-tech sub has a robot with a definite female voice and character and "she" is a weapon of war. It drugs, prods him and even probes his psyche, then announces it needs Jones's help. But Jones's problem is he needs to overcome his claustrophobia of dark places to save himself. And to save himself he needs to save the submarine. This story under the varient title "Son" in Strange Relations.