Shock Waves

The film opens as Rose is found drifting alone in a small rowboat. Two fishermen find it and pull her onto their own boat, barely alive and in a horrible state. Her voiceover indicates she had been rescued from some terrifying experience and the film's events are flashbacks of it.
Rose is part of a group of tourists on a small commercial boat. The Captain and his mate, Keith, share an attraction with Rose. Also on board are Dobbs, who is the boat's cook; Chuck, another tourist; and a bickering married couple named Norman and Beverly. After trouble with the engine, the navigation system goes haywire when they encounter a strange orange haze. The others sense that something is wrong. Norman in particular becomes abrasive. In the darkness of night, a hulking ship suddenly appears sideswipes their boat. The Captain sends up a flare, which momentarily lights up the eerie sight of a huge, rotting vessel wrecked nearby.
The next morning, everyone wakes to find the Captain missing. Realizing the boat is slowly taking on water, everyone evacuates in the lifeboat and makes for a nearby island. They see the huge wreck in the light of day; it appears to have been there for decades, nothing more than a skeletal framework, and now seemingly immobile, stranded on the island's reef. The group is startled to find the body of the Captain, apparently drowned while he was trying to check the underside of the boat for damage. They explore the island and discover a large, rundown hotel. At first they think it is deserted, but they discover a reclusive old man living there.
The man seems alarmed by their story, and he goes down to the beach to personally investigate. Under the water, strange zombie-like men gather, walking from the wreck along the ocean floor to the island. As Dobbs gathers items to help prepare food, the zombies corner him in the water and one of them attacks; before it kills him, Dobbs falls in a cluster of sea urchins and is horribly mangled. Rose discovers his body while swimming. Back inside the hotel, their reluctant host tells them that he was a Nazi commander in charge of the "Death Corps", a group of aquatic zombies. The creatures were intended to be a powerful weapon for the Nazis, but they proved too difficult to control. When Germany lost the war, he sunk their ship. Knowing the zombies have returned, he says they are doomed. The Commander goes down to the beach again and sees a few of the zombies off in the distance; they refuse to obey and drown him.
The others locate a boat that the Commander told them about and pilot it out through the streams to the open water. They lose control of the boat, and it sails away from them, empty. A zombie drowns Norman in a stream, and another chases Rose back to the hotel, where she kills it by pulling off its goggles. Chuck, Beverly, and Keith return to the hotel, and they barricade themselves in the refrigerator unit. The close quarters and stress cause the survivors to begin infighting, and Chuck accidentally fires a flare gun, blinding Beverly. Keith and Rose escape to an old furnace room, where they hide inside two metal grates, while Beverly hides in a closet. The zombies drown Chuck in a swimming pool outside.
The next morning, Keith and Rose discover Beverly dead, drowned in a large fish tank. Now on their own, they try to escape in a small sightseeing rowboat with a glass bottom. The zombies attack, and although Keith manages to defeat one by pulling off its goggles, a second one grabs him and drowns him just as the dinghy breaches the reef and drifts free. Rose sees Keith's lifeless body pressed up against the glass bottom of the boat and screams.
The film comes full circle, and Rose's voiceover returns. She is now in a hospital bed, seemingly writing in a journal. Her dialogue begins to repeat itself over and over, and she is revealed to be writing nonsense in her journal, apparently she has gone insane.

Question: Who was missing when everyone woke up?
Answer: The captain.