This story involves characters from Doctor Who mainly Amy Pond (Amy Williams after the Big Bang episode at the end of Series 5), Commander Strax, Madame Vastra, Jenny, Rory, Clara Oswald, River Song, the TARDIS with the current interior and the Doctor. It will also involve references from Doctor Who episodes before Doctor Who the Time of the Doctor Christmas special but will include events from the Doctor Who the Day of the Doctor. In the timeline sense Clara, Commander Strax, Madame Vastra, Jenny and River Song will be after the Day of the Doctor but before the Time of the Doctor. With the timelines of Amy and Rory set after they got touched by an angel and sent back in time by a weeping angel after the Angels take Manhattan episode and their farewell.
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Clara didn't know how she got here, strapped to a chair in a completely white room that seemed the size of her classroom back on earth. Clara did know that the doctor would save her though she had no idea of the time she was asleep, Clara looked around only to find one other chair similar to the one she was in and to her astonishment a small chested, slim redhead woman bound to the chair just as she was.
As the other woman was waking up she proceeded to thrash about in the chair obviously trying to get out. Clara thought she must try to calm this redhead down as whoever was behind this might want them to be still.
Before Clara could say anything to the redhead shouted "Rory, Doctor." This statement made Clara think maybe she was one of the doctors old companions. Clara remembered back at the black archive seeing a board filled with all the doctors former companions which included herself.
Clara searched her memory to see if she could recognise the redhead, from the angle Clara was at she couldn't see her face only her hair colour the only companions that came into Clara's mind was Donna Noble or Amelia Pond. Clara also recognise the name that she just called out before she said doctor, Rory then that meant that the woman with her was Amy Pond according to the name tag with the picture of them on the board in the black archive.
"Amy Pond?" Clara said
Amy calmed down and looked towards Clara before Amy said "I haven't heard that name in a while and only one person still calls me by that name and that is the doctor." Before long Amy realised that this person whoever she was knew the doctor.
"If you don't go by that name any more what name do you go by?" Clara asked.
"Amy Williams." Replied Amy.
Amy was relieved that the doctor managed to find a new companion although she was feeling confused as she knew that people meet each other from different time periods but she wondered how long the doctor spent alone before finding this person.
"Hi Amy glad to finally put a name to all the fantastic stories that the doctor told me, I am..." Clara started saying but before she could finish the sentence, Amy said her voice full of gratitude that although the doctor had found a new companion to travel all of time and space with that even the doctor didn't forget her.
Amy said "you're Soufflé girl! From the Dalek Asylum" Amy said to Clara, who upon hearing this blushed before she told Amy the story of how she ended up on the Dalek asylum.
The great intelligence and his plan to re write the doctors who timeline using the tear in his timeline that was in his tomb, in the huge TARDIS on Trenzalore. In order to deal absolute pain to his every breath, it had worked although she remained by the doctors side while every star went out.
According to Madame Vastra both Jenny and Strax were dead as the doctor wasn't able to get to them because of the great intelligence. So Clara took it upon herself to jump into the doctor's timeline to save him & everyone.
That meant that there were versions of throughout the doctor's timeline which included on the Alaska ship that crashed on the Dalek Asylum and in Victorian London when the doctor fought the great intelligence unfortunately she died then too.
Amy listened intensely at the story before she realised that the doctor chose her because she was caring enough to risk her own life to save everyone's lives, also that she was different then everyone else dying twice the only other person that died twice that knew the doctor was Rory.
As he dyed once by being absorbed by the light that came out of the crack in the wall. Also when he got touched by an weeping angel sending him back to 1938 at Winter Quay before him and Amy created a paradox that destroyed the weeping angels and winter Quay.
Clara then proceeded to tell Amy "Please call me Clara not soufflé girl, I am certain that wherever or whenever we are the doctor will find us." Amy agreed with that.
She knew what the doctor and Rory would do to save Amy though now that whatever had them, would not only have the doctor and Rory to deal with but whoever Clara knew. At that moment their captor showed itself although there was a hidden door directly ahead of them both Amy and Clara looked towards the hiss that came from the hidden door.
Both of the doctors companions were expecting an alien bent on using them to get the doctor, they were both surprised to see someone that looked like a human but if travelling with the doctor taught Clara and Amy anything it was never judge anything by their appearance what looked like a human could be an entity or alien.