They awake, soaking wet, on a metal floor. "Where are we?" Amy asks. "We haven't moved," the Doctor says. "We're in exactly the same place as before." They look around and find a wall of windows looking out over the pirate ship's deck. "It's a spaceship trapped in a temporal rift," the Doctor says. He gives them the lowdown on parallel universes sharing the same space in [on?] different planes. The reflections acted as gateways between the realities. The spaceship seems in pretty bad shape, dark and empty with bits of wire and electrical thingies hanging all over. They follow a beeping sound that turns out to have been the distress signal the TARDIS picked up earlier. As they wander through the ship, they can hear the Siren singing. A door slides open, revealing the dead body of the ship's former crew. The skull is elongated and toothy with a bony crest like a dinosaur. The lettering on his spacesuit reads "D.I.H.S."
After a start, the Doctor and friends skirt around the body and make their way into the ship's cockpit. Another dead crewman sits at the controls, slumped over in his seat. "How long has this ship been here?" Amy asks. "Long enough for the captain to have run out of grog," Henry says. He seems otherwise unperturbed. The Doctor sonics the corpse and says the crew were killed by human bacteria. He leans against the console, aiming for a casual pose but landing in a pile of alien snot instead. His hand comes away gooey. Somehow, even though the corpses are dry as the Sahara, the mucus is fresh as a daisy. For once, he's not infatuated with a discovery and wipes his hand down the sleeve of Amy's coat.
They wander next into the medical bay. Henry's crewmen are lying in beds suspended from the ceiling by wires. They're all alive but unconscious, hooked up to tubes and scanners. Henry rushes over to Moppet, Amy to Rory and the Doctor to the TARDIS. (The TARDIS is not lying on a bed, but stashed in a corner.) Henry moves to free Moppet, but the Doctor advises caution. The black spots, he discovers, are tissue samples. They start to disconnect Rory but the machinery beeps and he begins to struggle. The Siren approaches. The Doctor, Henry and Amy hide and watch as the Siren sings over Rory. He grows calm. "It's anesthetic," the Doctor says. "The music - her song - so she anesthetizes people then puts their body in stasis." The Siren moves over to Moppet. Henry whips out his gun and fires. The Siren turns all demon-red and shrieks at him. She growls and hisses, advancing on him until the Doctor sneezes. The Siren approaches him, her hands suddenly lighting up with fizzy fire. The Doctor talks himself into realizing it's a sterilization method. He blows his nose into a hankie and tosses it on the floor, where the Siren promptly sets it ablaze. He prattles on some more and then: "She's not a killer at all! She's a doctor!" She's a virtual doctor, running on autopilot, bringing the crew aboard to heal them. Kind of excessive for the paper cuts most of them had, but whatever.