Pirates return to their becalmed ship and are informed that there is a wounded man onboard. One of the pirates, McGrath, reports to the captain, Henry Avery, that the man slipped under the riggers and is likely to die. Avery notices a small cut on McGrath’s left hand and tells him that he’s a dead man, same as all the others. He grasps McGrath’s right hand, revealing a black spot on the palm. An unearthly female voice starts singing from somewhere and McGrath runs out to meet her, as the others realize the Siren is upon him. Avery locks his cabin door to seal himself and the others in, and wraps a medallion around the door handle. They hear McGrath’s final scream and then go out on the deck. McGrath’s gun is on the deck, but he’s gone with no sign of a struggle or a body. They hear a banging from the cargo hold door and approach it, and the Doctor, Amy, and Rory pop out.
The travellers are taken to Avery’s cabin, where the Doctor tries to explain in their terms that they sensed the ship in distress and came to help. Avery doesn’t believe it and accuses them of being stowaways, and explains that they’ve been stranded for eight days, becalmed. They make the Doctor walk the plank, explaining that they don’t have enough water for three more people. Avery puts Amy to work, figuring she won’t use many supplies, and Rory chastises them. A little. Once tossed below deck, Amy finds a sword, a hat, and a coat.
As he prepares to walk the plank, the Doctor points out that there is only a crew of five and asks where the others are. Before Avery can respond, Amy gets the drop on them. She forces Avery to drop his gun, but the captain warns that a sword could get all of them killed. One of the pirates tries to attack her by surprise, but once she fights back, they all retreat from her sword. She swings from a rope, cutting one man, De Florres, on the arm. He tells Amy that she has killed him but she doesn’t understand as De Florres looks at his right hand, where a black spot has appeared on the palm. Avery explains that one drop of blood and the Siren will rise out of the ocean to take the injured man. One of the crew manages to grab Amy and she drops her sword, scratching Rory. A black spot immediately appears on his hand, and Avery informs him that the Siren can smell the blood and has marked him for death.
The Siren begins singing and Avery tells them that’s how the Siren enchants its victims. Rory and De Florres fall under its spell, giggling, and Rory starts complimenting everyone. Avery explains that the song turns its victims into fools. A glowing female rises out of the water and lands on the deck. The beautiful woman reaches to De Florres, who eagerly goes to her. When he touches her hand, he explodes in a cloud of dust. Amy shoves herself in front of Rory and says that he’s spoken for, and the Siren turns demonic and shrieks, shoving Amy back. The pirates retreat to the cargo hold, and the Doctor grabs the bedazzled Rory and hauls him with them.
Once they’re safe for the moment, Avery explains that the Siren hunts ships laden with treasure, and has come after them since they were becalmed. The captain suggests that they depart in the Doctor’s “ship,” the TARDIS, and draws his gun. However, one of the pirates finds a leech on his leg and everyone quickly gets out of the water in the hold. The injured crewman realizes that he’s bleeding and a black spot appears on his palm. The Doctor insists that they’re safe, sealed in the hold, but the Siren materializes behind him. They try to hold the wounded man back, but he goes to the Siren and is disintegrated. The others retreat to the deck, taking Rory with him despite his objections.
The Doctor concludes that the Siren can use water as a portal, using a single drop of water to gain entrance. Avery suggests that they retreat to the ship’s magazine, which is dry as bone, and forces the Doctor and his companions to go with him. They discover that the key is missing but the door is unlocked, and they realize that someone already had the same idea. As they barricade the door, Avery finds a young boy hiding in a barrel. Avery explains that it’s his son, Toby. Toby, who has a bad cough and a fever, tells is father that his mother died of fever, but before she died she told him that Avery was a captain in the Navy. The boy came to join his crew, and warns that he can’t send him back. When Avery explains about the Siren, Toby shows him the black spot on his own hand. He doesn’t have any scars, and the Doctor concludes that the Siren is coming for all the sick and wounded, taking the weakest prey first. The Doctor decides they should go to the TARDIS, but Avery warns him that he’s not the captain. Toby opens a barrel containing water to get a drink and the Siren reaches out for him, and the Doctor manages to reseal the barrel.
The pirates are ready to give in, doomed by the curse, but the Doctor insists that they’re not helpless. He asks the captain for orders, and Avery puts his medallion of a siren on Toby’s neck. The captain then takes the Doctor with him and they try to make their way to the TARDIS, avoiding any chance of injury. Once inside, Avery goggles at the interior while the Doctor sets the controls.
The Boatswain decides that they’ve had enough and prepares to leave with the others, leaving Toby behind. Toby reminds them that Avery, a Naval officer, gave them orders, but the Boatswain explains that they’re pirates. The boy doesn’t believe them, and the Boatswain says he’s seen Avery gun down a thousand innocent men.
The Doctor tries to depart on the TARDIS but it doesn’t respond.
The Boatswain tells the remaining pirates to get what treasure they can and they’ll leave in the rowboat. Toby grabs a cutlass and orders them to stay at their post. When the Boatswain refuses, Toby scratches him.
The TARDIS is unable to get a lock on the time/space vortex, and is shaken by tremors.
The black spot appears on the Boatswain’s hand and he prepares to shoot Toby. Rory warns that a stray shot will set off the powder in the magazine. The mate, Mulligan, takes the Boatswain’s keys and departs.
The Doctor warns Avery that the TARDIS is having a tantrum and the controls are jammed. Realizing that the TARDIS is going to dematerialize, the Doctor gets Avery out just in time as it leaves on its own. They head for the magazine, but Mulligan draws a gun on them and gets around them, saying the Siren only wants Rory and the Boatswain. Avery goes after him since he’s holding the treasure, and Mulligan locks himself in a dark room. When he tries to strike a light, he burns himself, and the Doctor and Avery hear the Siren singing. They see her green light through the door and hear Mulligan scream. When the Doctor gets the door open, they find no trace of the man and no sign of water. Avery picks up a jeweled crown and the Doctor sees his reflection in it, and tells Avery that his theory about water was wrong. He explains that the Siren can travel via reflections.
Toby removes his father’s silver medallion, which reflects the light in the magazine.
The Doctor explains that the Siren attacks ships filled with treasure because it provides a perfect reflection from polished metal. They go back to warn the others.
The boy polishes his father’s medallion as the Doctor and Avery get to the door and yell to be let in. Amy and Rory let them in, and the Doctor breathes on the medallion to blur the reflection. He then runs through the ship, breaking every reflective glass surface, and explains to Avery that they have to dump the treasure into the ocean. Avery refuses at first but the Doctor reminds him that they have to protect his son.
The Doctor tells Rory and Amy that they have no choice but to wait until the wind picks up, and they can’t go on deck because in the calm weather, the ocean’s surface is like a mirror. Until then, they hide below decks. As they sleep for the night, Avery apologizes to Toby about the boy’s mother, and Toby says that she died three years ago and he has been waiting ever since. He asks what made his father turn pirate, but Avery ignores the question and tells him to get some sleep.
As Amy sleeps, she dreams of the eye patch woman looking at her from a hole in the side of the ship. The woman tells Amy that she’s doing fine and to stay calm, and then seals the hole. Amy wakes up but there’s no sign of the woman.
Avery finds the Doctor on deck looking at the stars. The Doctor talks of how traveling is lonely without a companion, and Avery says that if they escape, he’ll take Toby back to England because he’s not the father the boy needs. When the Time Lord wonders exactly who Avery is, a Naval officer or a rogue, Avery says that his course is set and he can’t alter it. The Doctor doesn’t believe it and says that things can change when one least expects it.
Amy finds the Doctor in the captain’s cabin and he says he can feel something out there, staring at him. A storm starts up and he tells everyone to mount the sails. Amy and Rory do what they can while the Doctor takes the wheel. Toby brings his father his coat and compass, but the jeweled crown falls out and rolls across the deck. It comes to a stop and the Siren emerges from its reflective surface. Entranced, Toby takes her hand and is disintegrated. The Doctor throws the crown overboard, too late, and the Siren disappears. He blames Avery, realizing that he was unable to give up gold for his family or his commission.
A mast swings loose, knocking Rory into the ocean. The Doctor stops Amy from going after him, and says that they have to release the Siren so that she will try and claim Rory, rescuing him. He opens a barrel of water and the Siren appears, and the Doctor tells her to find Rory. The creature dives into the ocean and the Doctor suggests that it’s an intelligent creature, and he hopes to talk with it in the hopes that all of its “victims” are still alive. He then proposes that they all prick their fingers so that the Siren will take them to wherever it took the others. Amy and Avery agree and they all prick themselves. The black spots appear and the Siren returns to claim them all.
The Doctor, Amy, and Avery wake up inside the control cabin of a spaceship trapped in a temporal rift, occupying the same space as the pirate ship but on another plane of existence. The reflections became gateways, and the Doctor tests his theory by throwing a piece of metal through the spaceship port so it lands on the pirate ship. A klaxon goes off and they realize that was the distress signal they picked up. Exploring, they find the dead alien captain, looking out into Avery’s quarters where the Doctor felt someone staring at him. The Doctor concludes that the Siren was a stowaway, and Earthborn bacteria came through the mirror portals and killed the alien crew.
Exploring further, the trio find a room filled with the crew of the pirate ship, all unconscious and strapped to tables while maintained by life support. Toby, Rory, and the TARDIS are also there. The comatose prisoners are all alive and well, and the Doctor realizes that the black spots are really tissue samples. He tries to free Rory, but they stop when they hear the Siren coming. As they hide, she enters the chamber and causes the awakening Rory to go back to sleep by using her song. When the Siren approaches Toby, Avery fires at her. The shot has no effect and the Siren takes on its demonic visage and advances on him. The Doctor sneezes and the Siren causes a fireball to appear between his hands. Thinking quickly, the Doctor sneezes into a handkerchief and throw it on the floor, and the Siren incinerates it and then advances on Amy tries to free Rory. The Time Lord tells Amy that the Siren is actually a doctor, and it reverts back to its beautiful appearance. The Doctor explains that it’s an automated medical program, and it’s been looking after humanity once its own alien crew died. She became a human doctor to tend to humans.
Amy and Avery try to free their loved ones, but the Siren refuses to let them. The Doctor has Amy show the Siren her wedding ring to prove that she is Rory’s doctor and can give medical consent. Crying, Amy asks to be near her husband and the Siren offers a glowing light. The Doctor explains that it’s a consent form and tells Amy to put her hand into the light. Once Amy does so, the Siren disappears and Amy shuts down the controls. Rory is unable to breathe without it and Amy hastily turns the life support machine back on. When Rory wakes up, the Doctor explains that he’ll die of drowning if he leaves. Rory tells Amy to show the Siren how to resuscitate him using CPR, and assures Amy that she can do it. When she asks why she has to be the one to save him, Rory tells her that he knows she’ll never give up.
The Doctor tells Avery that they have to free the spaceship. When the captain asks about his son, the Doctor admits that the boy is dying of typhoid fever and there’s no cure. Avery offers to stay with him and pilot the spaceship, having no home for him in England. The Doctor then goes to check on Rory, who assures Amy that she can do it. Amy agrees and they release Rory, who starts drowning again. They get him into the TARDIS and Amy applies CPR. She manages to revive him and they embrace.
Later, Avery pilots the spaceship away from Earth with Toby at his side and his crew behind him.
As Amy and Rory go to their quarters, the Doctor casually comments that he always worries about her. Amy remembers seeing his future self dying on Earth and says that the feeling is mutual. As the couple leaves, Rory warns Amy that they can’t tell the Doctor about his future. Amy says that she knows and they leave. Meanwhile, the Doctor studies the TARDIS scanner, which continues to show Amy as both pregnant and not pregnant at the same time.