The Doctor, Amy and Rory’s next adventure takes them to a 17th century pirate ship, commanded by the legendary-but vanished-Captain Avery. The ship appears to be under siege by a mysterious Siren, who places a black spot on her victims before lulling them and disintegrating them.
However, she is in fact teleporting them to a spaceship sickbay, to take care of their maladies-including Avery’s son-who has a fever-and Rory, who almost drowns. Able to free Rory from her, Avery and the ship’s crew take the spaceship to parts unknown.
In the next adventure, the Doctor is sent some unusual ‘mail’ in the TARDIS-A Time Lord cube, from his old friend the Corsair. The Doctor realizes that it means that apart from himself and the Master, it’s possible one or more other time lords survived the Time War, and are hiding in a bubble outside the known universe.
The Doctor lands on the planet, but unexpectedly the TARDIS’s AI is drained, and sent into the body of a young woman, Idris, a resident of the planet. The planet (Known as “House”), in fact, only holds four residents (Idris, “Auntie” “Uncle” and an Ood), and not a colony of timelords-and House is also sentient, and a TARDIS-eater-it’s killed the time lords there and lured others to feed on the TARDIses, and uses Idris as a suppository for their ‘minds’. He’s also used the remains of the time lords as repair material for Auntie and Uncle, to the Doctor’s horror.
Amy and Rory are soon trapped in the now powerless TARDIS-now possessed by the planet- and the Doctor must team up with Idris, who possesses the TARDIS’s heart and refers to the Doctor as her ‘thief’ (as he stole her way back). Working with his spaceship in the body of the woman, the Doctor and Idris are able to cobble together a makeshift TARDIS out of the remains of the other TARDISes, and go to rescue Amy and Rory.
Able to get onboard her ‘shell’, Idris gives up her mortal form and resumes life as the Doctor’s TARDIS, overriding and destroying House. She bids a tearful ‘goodbye’ as she once again becomes the ship’s AI.
In the future, people are using “Gangers”-quickly grown clones built out of a gooey substance.-through mind control to help dispose of acid, and keeping their regular bodies out of harm’s way. However, a freak electrical storm causes the ganger duplicates to gain sentience, as well as a duplicate of their host’s minds. The gangers then rebel against their flesh and blood hosts. The Doctor, stepping into the conflict, attempts to barter a peace, but factions on both sides aren’t having it. Especially one called Jennifer, who kills her original.
Even worse, the Doctor himself gets a ganger.
However, the Doctor’s double proves to be as honorable as his original, despite Amy’s initial distrust, and both Doctors are eventually able to broker a limited trust between the two, although not after a few deaths, including that of his ganger duplicate, who sacrifices himself to stop Jennifer’s rampage.
Back in the TARDIS, Amy is having pain. The Doctor says she’s having contractions, although she’s not visibly pregnant. The Doctor then tells Rory that the Amy that’s been with them the last few months, is in fact, a Ganger duplicate (although connected to the real Amy’s mind)an attempt to throw off the Doctor. He then disintegrates the Ganger duplicate.
The real Amy then wakes up in a white room, looked over by a sinister-looking woman with an eye-patch (That Amy has been spotting here and there with no explanation in past episodes). She’s also visibly pregnant, and about to give birth!