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When the Doctor came to after the Judoon had knocked her out during their transfer from the TARDIS she had no idea where she was.
For the first few weeks - or possibly months, she couldn’t be sure - they’d kept her in an isolation chamber. It was a small white room that she had been permanently suspended in the center of. Over time she could feel her senses shutting down - as she was sure was their intent - as the lack of external stimuli began to wreak havoc on her body.
By the time anything changed, she felt as if she was unconscious. Despite her vauge awareness of the Judoon guard’s arms wrapping firmly around her elbows as they harshly pulled her to her feet, she didn’t feel any of it.
They led her out of the chamber and into a hallway of the prison and as she leaned heavily against the Judoon guards, her brain entirely failed to process the things around her. She was vaguely aware of the limp steps her feet were taking and that the guards were grunting angrily as they yanked her alongside them, but nothing she saw or heard seemed to register at all.
It wasn’t until she’d been roughly thrown against the large slab in the center of a cell and the door slammed closed behind the Judoon that quickly abandoned her once more that she realized the stark contrast between the isolation chamber she’d been in and the rest of the prison was overloading her system. The pain started to creep in slowly at first, but before long she heard an agonized scream that it took some time to identify as her own.
As the Doctor lay limply on the stone slab in the cell she was only aware of one thing.
Everything burned.
Eventually - though how long it had been, she once again couldn't begin to guess -her thoughts started to sort themselves out and she did her best to take stock of her surroundings. It was nowhere she had ever been before which ruled out a number of maximum security prisons including Stormcage. As much as she’d hated it in the centuries she’d spent breaking her wife in and out of it, those centuries of experience would have given her an advantage in trying to get herself out of her current predicament.
Instead she found that there was little to be learned in her new cell. Despite the barred window at the edge of the room, there were no identifiable galaxies, planets, or even stars in view. The nearly black space outside only betrayed the existence of a few stars that were far enough away that she couldn’t even begin to guess where she was.
The atmosphere in the cell was equally uninformative. While the volumes of various gasses in the air would typically be a key indicator of a location’s placement in the universe, it was obvious that the air cycling through the prison was a fabricated mixture that was probably designed to facilitate a large variety of species while giving no indication of the location to any of the presumably dangerous inmates.
Even the gravity was unidentifiable, more like Earth’s than anywhere else despite Earth being an entirely impossible location to hide such a large structure without giving obvious internal and external indications of it.
Relenting to the fact that she still knew next to nothing about her surroundings, she tried to calm her nerves as she always had in situations like this - by reminding herself that it would only be a matter of time before someone came to help her out. But this wasn’t like all of the other times she’d been captured. This time there was no one who knew to come for her. The Fam would have assumed that she hadn’t made it off Gallifrey when she didn’t meet up with them as planned. The TARDIS was somewhere in deep space with no pilot and no trail to follow to rescue her. The only others in the universe that knew enough about the Doctor to notice her absence had no way of knowing she was missing rather than simply not with them, as she so often was.
For the first time in millennia the Doctor was well and truly trapped and as the realization settled the burning sensation came back in full force.
This time the sources of her overstimulation were easier to identify. The bright lights lining the hallway outside of her cell were buzzing loudly causing both visual and auditory frustration and that sound was accompanied by countless voices calling out for help that she knew must belong to the other prisoners. At one point she thought she could even hear the screams of a weeping angel in the distance, but that did more to make her question her own sanity than anything.
Perhaps that was for the best. After all, she didn’t even know who she was until the Master had told her and even now she didn’t know if she could believe him. Perhaps he had made it all up? Maybe this was all a trick? Were the Judoon working for him?
Of course, she knew that none of those things could be the case. She had known the Master longer than anyone else - or at least she thought she had - and the Master she saw on Gallifrey was in pain. He wasn’t there to hurt her with his lies, he had been there to hurt her because of her own.
But she hadn’t lied. She hadn’t known. She still didn’t know.
The only thing she could do was wait for something to change. Eventually, someone or something would give her information that she could use to escape. Of course, even if that didn’t happen she would escape eventually. A lifetime sentence doesn’t mean much when you’re immortal. In the long run it wouldn’t matter who came and went, she would apparently outlive them all.
Whether she wanted to or not.