I think there was an original timeline the Silence messed up, this is it. The chapters will be posted in no particular order. Cross posted on Ao3.

Oren Jayce simply wanted a night out. Go to a party, meet some people..relax. Instead he wound up meeting a strange red headed woman calling herself The Doctor and being chased by a shapeshifting alien assassin into a strange tall blue box. The inside of which he was totally not expecting..

Florm Rox Fey Fenerill-Slam Slitheen had lost her hunt with Sarah Jane Smith. But luckily, just before the lights went out, the Slitheen was able to find someone else that they could use as bait. This is their story.

All that Time Lord knowledge was stuck in Donna's head, and only the Time Lords could help the Doctor fix her. Of course, they're really going to hate the idea. They also hate him. And humans. They're really, really going to hate that he's married to one. Talk about a tricky home visit. Oh, and to top all: he also has to bring Jack along. (Eleven/Rose, part 9 of "Consequences")

The Doctor finishes his sentence in School Reunion.

Klary Cedrics was an introverted young woman visiting the UK for the first time. On a visit to the Doctor Who Experience in Cardiff, she ends up transported to the Whoniverse, set to jump through the Doctor's timeline. She must overcome her fears and learn to trust as she travels throughout the universe and even experience romance along the way. (9-15/ maybe some Old Who)

What if the doctor was able to rescue Amy from Demons run, what if he was able to find Melody as a baby. What if he was able to snatch her from Madam Kovarian? What if River was rescued by her parents. How would River turn out? How would her bond with the doctor change? River/Eleven, Rory/Amy, Parents Amy/Rory, fluff, feels, fix it, Minor Jack Harkness, Minor Martha Jones

The story of Vastra, Jenny and their growing family through the twentieth century as they face new and old enemies, friends, and everything in between. A few characters are owned by BBC or History books. [[ A work in progress ]] Please Follow as I am updating the story as soon as I have time.

What happens when the TARDIS has to intervene to save the doctor and their future? Who will the TARDIS bring in? What will the TARDIS do? While in prison the Doctor has too much time to think, who are they? What are they? Are they even still the Doctor? The Doctor may not know who they are anymore but they have had many friends through space and time that are willing to help.

Phoenix has been left on Earth and the Doctor has just regenerated into a completely new man. Nothing is as it seems and the one who has been hunting Phoenix is only drawing nearer. How will the two aliens react to the many changes within themselves and each other? Who is behind the attacks on Phoenix and who killed her mother? Find out here.

While Rose is hopping through dimensions and unfortunately lands on the SS Madame de Pompadour.

Alyssa has always been a fan of Doctor Who. One day she is teleported to the Doctor Who universe where she constantly jumps through time. Mainly to adventured The Doctor goes on but also those who are connected to him. (I'm not really good at writing summaries but this best explains my story)

The Doctor and Bill are summoned by UNIT to investigate a strange discovery in Egypt. What they find beneath the sands could mean the end of the world.

When I was younger, I always dreamed of being able to just go out there and see the world. And despite my initial panic about having died and been reborn as an abandoned injured pet, I felt almost excited. Then, I met the Doctor. "You're just a small fella aren't you? Just small and scared and alone. I know how that feels."

(Synopsis: A Slitheen Family of thieving criminals crashland on Earth. Faced with an uncertain environment and hostile natives, this Family hatches a cunning plan to enrich themselves: stealing all the alien technological assets that UNIT possesses before they repair their ship and head back out into space once more…) (N.B. This is a Slitheen story with mature and adult themes.)

Rose Tyler's life is a grand series of adventures, but her friends and family are often left behind. yet they see and know things that even Rose or the Doctor do not. This story will hold the introspections and missing scenes of the Guardians of the Universe Series.

Many years after his adventures in Time and Space with the Detective Boys, the Doctor lands in a forest on the Tatras Mountains, Poland, 1932. There he meets Mariah, Karin, Gregor and Anatoly, a group of 4 friends emigrating from Ukraine, in a cabin owned by a mysterious man who's hosting them. Things soon will degenerate when the food supplies ran out and a storm flood the cabin.

After saying goodbye to Rose, the Doctor throws himself into his travels in an attempt to distract himself from thoughts of his lost companion. With a little help from the TARDIS, he is finally given the space he needs to grieve. (Set after Doomsday, between seasons 2 & 3)

The year is 1800, and the TARDIS crew end up on the USS Pickering, setting sail inside the infamous Bermuda Triangle. However, there is a reason why the triangle is as infamous as it is: a monster resides there, waiting to destroy any intruders who come by and erase any evidence of it existing. It is known by the name of the man known to have sacrificed his own son: Tantalos.

A girl just wants to live. The Doctor has other plans. (In which James ends up in Doctor Who, for Christ's sake, and is dragged around by a pretty boy she is not falling in love with. Not.)

Two heads may be better than one, but they're also a lot more trouble when those heads have been turned into children thanks to a run in with a time flare. Now Yaz and the Ponds are left with two time-lord toddlers, with the only available cure being the mythical fountain of youth. And Eleven and Thirteen are unlike any children they've ever seen. RATED T Just in case

Sally and Vince help a new friend fight an old evil.

After the dream with the Mara, Tegan shuts off everyone until one day she gets a visitor promising to help her find her lost love.

There is a house in Santa Fe, New Mexico with strange secrets buried within its walls, secrets that could lead to the collapse of the Multiverse. An unusual family has gone missing, yet their voices can be heard crying out for help across space and time. Who will answer the call? The Doctor and Donna Noble, of course. And, coincidentally, a dimension-hopping Rose Tyler.

With the assistance of some strange plants surrounding the TARDIS, the Doctor and Rose are finally able to express their feelings for each other.