Prisoner Zero

Prisoner Zero was a multi-form shape-shifting alien, held prisoner by the Atraxi for unknown crimes. He later escaped to Earth when the TARDIS explosion caused cracks throughout time and space, hiding in an extra room of Amelia Pond's home for 12 years. Said amount of time later, he was tricked into revealing himself by the freshly regenerated Eleventh Doctor and recaptured by his jailers to be executed. Before being taken away, he subtly left the Doctor a parting warning about the Silence.

Biography
In 1996, Prisoner Zero was a captive in an Atraxi extra-dimensional prison. When a crack in the universe opened into Amelia's bedroom wall, it was able to escape. Prisoner Zero hid within a room in Amelia Pond's house in Leadworth, placing a perception filter on the door to the room so that it would never be found. It hid on Earth for twelve years, watching Amelia grow up and sometimes venturing out into the village, posing as comatose people admitted to Royal Leadworth Hospital whom it had established a psychic link with, a process that took months. If the person it was copying was dreaming about having someone else with them, Prisoner Zero would appear to be multiple lifeforms touching each other, while actually being one creature with many limbs and orifices. Since the forms it took were of comatose people, in 2008, Rory Williams, who worked at the hospital as a nurse, took pictures of them with his cell phone, knowing that the people he saw shouldn't be up and about. It was during this time that Prisoner Zero established a Psychic link with Amelia (later Amy) Pond.

The Eleventh Doctor belatedly returned to Amelia's house to save her from the multi-form. After Amy had seen its natural form, Prisoner Zero took a shape-shifted form but was confused as to which voice to use for each form. The Atraxi, who had followed the Doctor, broadcast a global warning that they would incinerate "the human residence", Earth, if Prisoner Zero did not surrender. After escaping from Prisoner Zero, the Doctor and Amy went into the village square, where residents of Leadworth were taking pictures of the Sun, obscured because the Atraxi had put a force field around the Earth. The Doctor noticed that Rory was facing the other way, taking a picture of Prisoner Zero, who was disguised as a man with a dog. The Doctor attempted to draw the Atraxi to Prisoner Zero by overloading all the electrical devices in the surrounding area with his extraterrestrial sonic screwdriver, but the screwdriver burnt out and Prisoner Zero escaped again.

Prisoner Zero arrived at the hospital and proceeded to kill all the doctors and nurses. It then took the form of a woman with two children to fool Amy and Rory, but gave itself away by talking with the woman's voice through a child's mouth. It snarled at Amy and Rory and chased them down the corridors. The Doctor arrived through the window just in time, and revealed his master plan to Prisoner Zero.

Believing that surrender would mean execution, Prisoner Zero said it was prepared to die in flames with the whole planet. The Doctor suggested Prisoner Zero open another crack to escape, but Zero replies the cracks were not its doing, but cracks in the skin of the universe, and taunted the Doctor about his lack of knowledge. "The Doctor in the TARDIS doesn't know." He then added to that,"The Pandorica will open. Silence will fall". When cornered by the Doctor, who had given the Atraxi its location and pictures of all its previous disguises, it tried to avoid Atraxi detection by using a psychic connection with Amy to imitate her younger self and the Doctor. The Doctor thwarted this by stimulating Amy's recent memory of Prisoner Zero and forcing it to take on its own form. The Atraxi detected and secured Prisoner Zero, as it gave its final warning: "Silence, Doctor. Silence will fall". (DW: The Eleventh Hour)

Though the cracks in time were negated (DW: The Big Bang), some of the event may have still occurred, as the Doctor in the rebooted universe still chased the Atraxi off the Earth and called them back to scold them, as he did for them threatening to incinerate the Earth with Prisoner Zero on the surface before the reboot. (DW: The Eleventh Hour, A Good Man Goes to War)

Behind the scenes

 * In an issue of Doctor Who Magazine, Matt Smith and Karen Gillan referred to Prisoner Zero as a "Face Tendril". Steven Moffat also referred to it as such.
 * Despite being the first villain of the Matt Smith era, Prisoner Zero wasn't seen in any trailers or publicity images.
 * It is unknown what crime(s) Prisoner Zero committed in the first place. Steven Moffat's DVD commentary on The Eleventh Hour reveals that there was originally a line of dialogue establishing that Prisoner Zero had impersonated an army and invaded a planet, but the line was cut. Moffat states that he was never quite happy with the explanation and it is better left to the imagination.
 * Prisoner Zero's entire body in its true form is never seen, always trailing off-screen.