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As his given title would suggest, Prisoner Zero was a captive of the Atraxi, imprisoned within an extra-dimensional prison. At one point, he was able to escape through a crack in the universe, arriving in Amelia Pond's house on Earth. Prisoner Zero hid itself within one the rooms of Amelia's house, placing a Perception filter on the door so she would not notice it. He remained in hiding for twelve years, occasionally venturing outside by taking the form of those he made a psychic connection with, rendering them comatose as a result.
When the Doctor returned to Amelia (now calling herself Amy)'s house, he brought the Atraxi with him, who threatened to incinerate the whole planet if Prisoner Zero did not reveal himself. Realising that turning himself in would mean execution, Prisoner Zero ran, preferring that the entire planet die with him. The Doctor and Amy tracked him down to the local hospital, Prisoner Zero taunted the Doctor, telling him "The universe is cracked. The Pandorica will open. Silence will fall". In a last-ditch attempt to avoid Atraxi detection, he then made a psychic connection with Amy, taking on the form of her young self with the Doctor. The Doctor made his own psychic connection, making her think of Prisoner Zero, causing him to take on his own form. The Atraxi located and killed Prisoner Zero, but not before he told the Doctor "Silence will fall."
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