A Brief History of Nearly Nothing: A Doctor Who Fanfiction

Everyone knew the story of Rose, it was simple, and easy to remember since it was so profound. He grabbed her hand and yelled run.
That's was how Torchwood recorded the files, that is. But, there was someone else in the shop that night, someone never mentioned in the files, because the Doctor had erased any and all trace of them. Their name was never mentioned, their personal files gone, never to be seen again. Someone who was under his protection.
No one knows why the Doctor erased their files and not Rose's, and of course he's never in one place long enough for any one to ask him.
The only two beings in the universe who could tell us, were the most impossible to reach.
The Doctor, a man so alone with nothing but a blue box of hope and screwdriver as his only possession.
And, the companion, the universe forgot.
Jack Harkness often speaks of them, never naming them out rightly, but from what I have gathered in my research, the missing files involves a female that was closer to the Doctor than any other companion had been and possibly would be.
She was said to have accompanied the Doctor for most of her life, if not all. There were whispers and rumors that she was more than just a companion. Rumor had it, depending on which one you got, that she was either a sister, a lover, or a mother. Jack Harkness was the only one on earth who knew the story, though if you asked him, he only knew what little he was allowed to know, and even then, it wasn't much,
The mystery of this forgotten companion, runs rampant to this very day.
My name is Nova Hawthorne. I am Torchwood's official recorder, and I have been tasked with discovering the story of the missing companion.

Book 1