Back in the magazine, the injured pirate pulls out a gun, ready to shoot Moppet. Rory sensibly points out if he shoots, he'll blow them all up. The one uninjured pirate makes off with his comrade's keys. Amy says, "No honor among pirates," like she's disappointed. They're pirates, not Boy Scouts.
The TARDIS is having a tantrum. I'd do the same if a grubby, crusty old pirate put his hands on my astrolabe. The Doctor fiddles with various controls and spouts off things that only make sense to him. "I'm almost out of ideas!" he shouts. "Well, we could try stroking her and singing a song." "Will that help?" the captain asks hopefully. Depends on who's doing the stroking. There's lots of stumbling about and flailing and noise and the Doctor's worried that the TARDIS will dematerialize and they'll end up who-knows-where. He grabs the captain and runs. "Abandon ship!" As soon as they've cleared the doors, the TARDIS fades away in a shower of light and groaning of gears. The Doctor stands there for a bit, wondering why the TARDIS would run off on its own. Maybe because it's tired of being in a gross ship full of gross pirates?
On their way back to the magazine, the Doctor and the captain run into the mutinous pirate Mulligan. He waves two guns at them as he runs past. "He's got the last of the supplies; we should go after him," the Doctor says. Supplies of what? The captain is more concerned about the jewel-encrusted crown Mulligan is making off with. He locks himself a storeroom and promptly burns himself when he tries to light a torch. The Siren starts singing. On the other side of the door, the Doctor and captain see the eerie green light and hear Mulligan's scream. The Doctor sonics his way inside. The captain immediately grabs the fallen crown and practically hugs it in relief. The Doctor peers at his reflection in the gold of the crown. "I was wrong," he says. He talks himself through a revelation, starting with realizing that the Siren only came through still water and ending with the realization that she can come through any reflective surface. A quick cut to the magazine shows Moppet, sitting with Amy and Rory, polishing his shiny new mermaid charm. She should have come for him by now, but it's not in the script. The Doctor stuffs the crown into a bag and they run off to warn the others.