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)

Entrapment
On an adventure with his companions 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 Lords 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 humans 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 Handbots who detected her unregistered human bacteria and attempted to apply their medicine to her. As the medicine was designed for Apalapucians, it would kill Amy as a human. Amy managed to avoid the Handbots by hiding in the exhaust from the temporal engines 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 engines 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)

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 Handbots 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)