Clockwork is your average stallion, hard working, dependable, maybe a bit obsessive about the placement of his tools of trade. One day after a long afternoon of attempting to fix a clock he receives an uninvited visitor in the form of a confused (and confusing) grey pegasus known only as the Doctor. Now he and the Doctor, still adjusting to a completely new body, must find the Doctor’s missing friend and try to adapt to each other as best they can. Little do either of them know that a dark shadow watches from behind it all and will do everything it can to make this the Doctor's final adventure.

This story is a sequel to Wolf at the Door

In the aftermath of the Bad Wolf seizing control over the 9th Doctor's body, The Doctor's past self and everypony else involved with the incident in the matrix must look for a way to free the Doctor from the Wolf's corruptive power.

Meanwhile, the Wolf has been busy wreaking haphazard vigilante justice across the galaxy, and now threatens to bring the battle to the home front as Equestria enters the 21st Century.

This story is a sequel to Dinky Who

Pinkie Pie meets Doctor Whooves for the first time. He cleverly lies and says his name is Time Turner and he fixes clocks. He's surprised when she approaches him with a pocket watch...wait...those marks...is that Gallifreyan?
-----------
Author's note: It's best to be a Whovian if you are to read this. While I try to write this as simple to understand as possible, it just makes the story a better read.

Also, this Doctor Whooves is based on The Doctor from the Doctor Whooves and Assistant series. This point is after Appleoosa and prior to the events of Wrong Way Backwards. Familiarity with source material will make the story better.
Thank you.

This story is a sequel to Survival of the Cyberponies

When the TARDIS crashes into the TARDIS from the past, an old Doctor and the newest Doctor come face to face. Something is not right, and the current Doctor can feel it. An old enemy threatens a village of ponies, and the Doctor discovers the truth about the Bad Wolf.

This story is a sequel to Stranded in a Lost World

Team TARDIS takes a break from adventuring, and the Doctor decides to grant destination requests. Derpy chooses a remote alien beach first, then Lyra votes to visit a space station far into the future. Beneath the glittering streets and markets of the futuristic city in space lies one of the Doctor's oldest enemies trying to recover from the brink of destruction.

This story is a sequel to Election Day

For Lyra's first "proper" trip in the TARDIS, she wanted to see one of Equestria's starships. But as the TARDIS crew lands on the ship, they get a not-so warm welcome. What's worse, a temporal distortion hurtles the starship back in time and out-of-control! With less than a day on their hooves, the crew of the starship and the crew of the TARDIS must work together to get the ship working again, or risk being stuck in the Late Cretaceous with flesh-eating dinosaurs!

This story is a sequel to Timeswirl

When Derpy decides to drop in to visit home, she discovers that she's been gone for longer than she intended, and another young mare expresses interest in joining the TARDIS crew. At the same time, something is very wrong with the mayor of Ponyville as he seeks re-election, as well as other ponies throughout the town. It's up to the Doctor and his two companions to find out!

This story is a sequel to The Iron Army

The TARDIS crash lands in the middle of Pre-classical Equestria, before Equestria itself even exists!

Trouble is brewing. Things are starting to happen decades before they are supposed to, and the player that could otherwise bring the tribes through these difficult times have yet to take center stage. Why are the windigoes so active, and where are they coming from? It's up to Derpy Hooves and the Doctor to find out!

This story is a sequel to Symbiosis

Adventuring to the 30th century, a quick side trip turns grave as the Doctor and Derpy find themselves in the middle of mysterious earthquakes that only affect single buildings, and touchy robots with deadly tendencies. With the help of Luna herself, they set out to uncover the reasons behind these strange phenomena only to discover a plot against Canterlot itself. The TARDIS crew and Princess Luna must find a way to stop this mysterious mare before innocent lives are lost at the steel hooves of her robot army.

FANTASTIC!

In the year 1999, a young mare is abducted, but is saved from a terrible fate by a mysterious stallion called the "Doctor". Derpy wonders why she was wanted, who this "Doctor" is, and what has been happening to cause the disappearance of ponies across the country. As the seemingly alien kidnappers continue to follow her, Derpy must team up with the Doctor in order to save her own life- and the life of everypony around her.