Author's Note: I DO NOT OWN DOCTOR WHO! This is a work that is an AU from the television series that will follow some plot lines with a twist.
Prologue
The Last Great Time War
"My Lady!" a young guard screams as he enters the chamber of Celestia, known as the Queen of time. She rules over all Time Lords and Ladies on the planet Gallifrey and is the only living being to be able to control the time vortex. Old legends say that the vortex chose her when she was a child preparing for the academy. When she looked into the vortex a part of it went into her body giving her the power to control time. He was followed by his commanding officer.
"Yes Lieutenant, what is it?"
"Daleks! Thousands! They will be on us in two hours."
"Assemble the troops! We shall meet them head on!" As the young guard ran out, his captain stayed behind.
"Captain, Make the preparations for the Ark"
"Yes, My Lady" and he leaves the room.
Celestia turns toward the windows and prepares herself for what needs to be done.
Finally, she turns to a maid "Planitina" and the maid nods her head.
"I'll fetch him My Lady." And quickly flees the room.
A few moments later a Time Lord, known only as the Doctor, stands before the Queen.
"Celestia, what's going on? Everyone is going crazy outside."
"The end is coming, I can see it."
He grabs onto her shoulders "I don't understand…What does that mean?!"
She hesitates. "Daleks."
He is still clutching her shoulders but the grip is loosened.
"What are you going to do?"
"I'm going to do what it takes to protect my people. Which is why I brought you here..." She hands him a key. "…I want you to take this key to the last living TARDIS and leave as soon as you can. I may be able to stop the Daleks but if I can't you know what must be done."
The Doctor becomes angry. "Have you lost your mind? I can't leave now!"
She smiles to herself. "I knew you would say that, nevertheless, the time is drawing near, the end is approaching and I need you to live."
"You keep saying that…the end of what?"
She looks up at him with tears in her eyes. "Time"
Before the Doctor could say anything the captain returns to the room "My lady, it is ready"
"Thank you Captain, I shall be there in a moment." He leaves and she turns back to the Doctor.
"You need to leave now Doctor, leave while you still can."
"I won't leave, not without you!"
"Oh Doctor…If only I could." She pauses and freezes time. "Goodbye my love." She kisses his cheek and leaves the room resuming time. The Doctor is alone in the chamber. He rushes to the window and sees Celestia standing on a hovering metal disc confronting the Daleks.
This is it she thought. The Daleks are right in front of her and are about to strike. "I give you a choice, leave in peace now or suffer."
"EXTERMINATE TIME QUEEN!"
"I thought you might say that" she hits a button on the pad and a metal wall begins to form around her. Some sort a vacuum begins to suck the Daleks into the walls and are sealed off, the Queen included.