Also genderBent Danny au as well, because it’s my au idea and I can do what I want!!
The Doctor had a little sister. She was significantly younger than him. Still a child by Gallifreyan standards when The Time War started. Despite the massive age gap The Doctor absolutely loved his little sister!!! She was the light of his life. It broke his hearts when he thought she’d died with the rest of his people.
What he didn’t know was that someone (not sure who, maybe one of their parents, or maybe even the Master?) Knew the Time War would be the end of them and decided to save her (or in the case of The Master, to maybe use her in the future as a pawn against the Doctor?). They used a Chameleon arch on her, turning her human. (When she’s turned human she winds up looking like an infant.) and then they send her off to Earth.
The Doctor’s sister, now newly human, winds up getting adopted by the Fenton’s and is given the name Danielle. She grows up on Earth with no memories of her life on Gallifrey, though sometimes (thanks to her fob watch with her memories in it) she dreams of it. And then the portal accident happens and she’s made half ghost.
About a year after the portal accident the Fenton parents find out about her being half ghost. They do not take it well. They attack her, injuring her, and she goes on the run. One day, while sitting in a park, the Tardis appears, and Dani approaches it. She has this vague recognition of it but doesn’t understand why she feels this way about this blue box. And then The Tenth Doctor and Donna step out.
Ten immediately lights up at seeing her and swiftly pulls her into a hug, spinning her around saying how happy he is to see her. And then he stops and asks why she’s not in Cardiff and where the hell is Jack. And then pauses when he realizes she has no idea who he is. He brings her into the Tardis and explains that she’s really a Gallifreyan, and her Gallifreyan memories and biology is hidden in her fob watch. That she’s his younger sister. And that a younger him met her sometime in her future.
He takes her to Cardiff, several months before the first season of Torchwood, and drops her off with a note for Jack and directions to the Torchwood 3 base. She makes her way there, entering through the tourist information centre. Ianto is there behind the desk and she tells him, while looking straight into the camera in the corner of the room, that she has a message for Jack from The Doctor. The phone rings immediately and when Ianto picks it up Jack tells him he’ll be up in just a minute and to not let Dani leave before he gets there.
When Jack gets up there Dani immediately hands him the note from the Doctor. The basics of the note is: we’ll (Jack and the Doctor) meet again sometime soon. But for now he has a favor to ask of Jack. The girl, Dani, who gave him this letter is his (the Doctor’s) younger sister. She’s under a chameleon arch at the moment so she’s human and doesn’t remember being a Gallifreyan. And he requests that Jack look after and protect her to the best of his abilities.
Jack reads the note over three times, looks the kids in front of him over, and immediately decides to adopt this tiny child. The Doctor asked him to look after and protect her so he damn well will!!! Plus the kid is tiny, scrawny, and just looks to be in the worst shape. She’s covered in scars (both from her time being a hero and from when the Fenton’s attacked her after finding out about her halfa status), and she’s got this skittish look in her eyes. And she’s horribly thin, wearing clothes much to big for her. Yeah this is Jack’s new daughter, and may the universe have mercy on the soul of anyone who fucks with her, because he sure as hell won’t.
Dani is enjoying life as Jack’s new adoptive daughter. After a while she even feels comfortable enough to tell him about the Fenton’s and her powers. He takes her powers pretty well, but does not take to well to finding out about the Fenton’s and what they did to her. Season 1 of Torchwood comes around with Dani being part of the team.
And then Doctor Who S3E11 “Utopia” comes around. Dani winds up hitching a ride on the outside of the Tardis with Jack when it gets flung to the end of the universe. This is when the Doctor meets Dani for the first time. Immediately upon Jack reviving at the end of the universe Jack and Dani explain who she really is to the Doctor. When he realizes that Dani is actually his little sister the Doctor pulls her into a bear hug, burying his face into her shoulder to hide his tears. He’s absolutely ecstatic that she made it out of the Time War alive.
The rest of the episode goes the way it does in the show just with Dani there. Not sure exactly how her presence would affect the events of the sound of drums and the last of the timelords. Haven’t thought that far ahead yet. But I imagine her ghost powers would be a bit of a hinderance to the Master’s plans. Unless the Master, during his 8 months on Earth, gets in contact with the Fenton’s and gets some ghost weapons. But again haven’t really thought that far ahead for this idea!