Alternate timeline ( The Girl Who Waited ) In an alternate timeline , Amy Pond was trapped for thirty - six years in the Two Streams Facility on Apalapucia . ( TV : " The Girl Who Waited " ) History . Entrapment . On an adventure with his companion s Rory Williams and Amy Pond , the Eleventh Doctor decided to take them to Apalapucia , the No . 2 destination for the discerning intergalactic traveller . However , the Doctor was unaware that the planet had become infected with the Chen - 7 virus , a deadly disease that killed those that got infected in one day . In an act of kindness , the Two Streams Facility was set up on the planet where those infected would be put into compressed time streams to live out their lives while only a single day of absolute time would progress outside . When the Doctor and his companions arrived , Amy went back to get her phone from the Doctor ' s TARDIS and as a result , was not with the Doctor and Rory when they entered the Green Anchor time stream which was the regular time stream of the facility . As a result , when Amy attempted to follow them , she accidentally entered the Red Waterfall compressed time stream . While the three attempted to figure out what was happening , a week passed for Amy in Red Waterfall . Finally , the Doctor and Rory learned about Chen - 7 from a Handbot , a disease that was fatal to two - hearted beings such as Time Lord s like the Doctor . With an understanding of what was going on , the Doctor ordered Amy go deeper into the facility to find a safe place while he took the time glass to lock onto her time stream and rescue her . As human s and thus beings with only one heart , both Rory and Amy were immune to the virus , but the Doctor was not and so could not enter the deeper areas of the facility . ( TV : " The Girl Who Waited " ) Thirty - six years alone . Following the Doctor ' s instructions , Amy made her way deeper into the facility and began exploring . However , she was found by Handbot s who detected her unregistered human bacteria and attempted to apply their medicine to her . As the medicine was designed for Apalapucian s , it would kill Amy as a human . Amy managed to avoid the Handbots by hiding in the exhaust from the temporal engine s and continued her explorations , meeting the facility ' s Interface . With the Interface ' s help , Amy found a safe hideout by the temporal engines themselves where the Handbots could not detect her . As requested by the Doctor , Amy left him a message pointing to her location with lipstick on the door to the temporal engine room . Trapped and waiting for rescue , Amy began to adapt to life in the Two Streams Facility . Amy managed to reprogram the Interface to answer any question she wished , but could not get it to tell her how to escape . Amy adapted fighting techniques for the Handbots , eventually managing to fashion armor out of a destroyed Handbot and obtained a sword and club . She created a sonic probe to help with her tasks . As time passed and the Doctor failed to arrive to rescue her , Amy grew bitter and began to hate the Doctor . Needing company , Amy " disarmed " a Handbot that she named Rory and turned it into her pet . ( TV : " The Girl Who Waited " ) Refusing to help . After thirty - six years , the Doctor and Rory finally arrived in Amy ' s time stream due to the TARDIS locking onto Amy at the wrong point in the time stream and causing them to arrive when she was old instead of young . After Amy and Rory were reunited , the Doctor devised a plan to use the temporal engine s to fold the two parts of Amy ' s time stream and bring her younger self into the present . The old Amy refused to help them as it would mean that she would be erased from existence . Though Rory was able to use the time glass to allow the two Amys to communicate , the old Amy steadfastly refused to help rescue her younger self , ultimately forcing the Doctor and Rory to leave with the aged Amy . ( TV : " The Girl Who Waited " ) Negation . Changing her mind . As in the original timeline , the older Amy refused to help the Doctor and Rory rescue her younger self from the past as it meant that she would never exist . However , this time when Rory used the time glass to enable the two Amys to communicate , the older Amy remembered the conversation and the fact that it was her own future self ' s fault that she had gotten trapped , not the Doctor and Rory ' s . The two Amys , who both loved Rory deeply , reminisced on their love for him . This time , the younger Amy managed to convince her future self to help save her . After her conversation with her younger self , the older Amy agreed to help the Doctor change history and save the younger Amy . The Doctor suggested that Amy witnessing the way things went the first time allowed her the chance to change her own future . The older Amy ' s one demand was that the Doctor bring her with them in the TARDIS so that she could continue to exist after the rescue was over . Though the Doctor admitted that it would be difficult , he claimed that the TARDIS could sustain the paradox of two Amys existing at once . With the two Amys working together , the Doctor and Rory managed to use the facility ' s temporal engines to bring the younger Amy forward to their current point in time . ( TV : " The Girl Who Waited " ) A hard choice . After the group succeeded in bringing the young Amy forward in time , the Handbot s attacked them . After disabling three , the two Amys and Rory attempted to flee to the gallery section of the facility where the TARDIS was parked , but were forced to fight off more Handbots along the way . During the fight , a Handbot knocked the younger Amy unconscious before Rory could disable it which forced Rory to carry Amy back to the TARDIS . At the same time , the older Amy stayed back to fight off more Handbots . After Rory made it aboard the TARDIS with the younger Amy , the Doctor locked the older Amy out . The Doctor explained that he had lied and the TARDIS could not sustain the paradox of two Amys at once . As a result , Rory had to choose between the younger Amy and the older Amy as he could not have both . As the older Amy demanded entrance to the TARDIS , Rory was conflicted about what to do . The older Amy ordered Rory to keep her locked out if he loved her and Rory reluctantly complied . Rory and the older Amy had a final conversation in which Amy encouraged Rory to live his life with the younger Amy and willingly gave up her existence to ensure her younger self ' s chance at that life . With the Handbots approaching , the older Amy had the Interface show her an image of the Earth and accepted her fate , allowing the Handbots to sedate her and give her their deadly medicine . As the Handbots moved to kill the older Amy , the TARDIS dematerialised . With the younger Amy having been rescued , the timeline where she spent thirty - six years trapped in the Two Streams Facility ceased to exist as did the older Amy Pond . ( TV : " The Girl Who Waited " )