1000 years ago, there was a small Unicorn kingdom up north called Ice Draught, and the young Queen Zima had a governess named Clearwin. When Clearwin was about to die on Hearth's Warming Eve, she was taken away by a mysterious stallion called the Doctor and his magical blue TARDIS. 1000 years later, Equestria is a frozen Hell where a dwindling number of ponies are hunted down by the ghastly Dark Ones. The Doctor and Clearwin are trapped in this nightmare, and must learn the truth of what happened if they are to escape. An adventure featuring the Eleventh Doctor, as played by Matt Smith.

A celebration of 50 years of Doctor Who, season 4 of Friendship is Magic and the Christmas season. For the Doctor, takes place in between "The Angels Take Manhattan" and "The Snowmen". Made to introduce new readers to Doctor Who.

Soundtrack: Music picked for the story. Updates with the story. All tracks by Murray Gold.

Nightmare for Eleven: The beginning.
TARDIS Emergency: A problem with the TARDIS.
Clearwin: Clearwin's theme.
Sombra: Sombra appears.
Clearwin and the Doctor: Clearwin shares a moment with the Doctor.
Frozen Equestria: Exploring the dying Equestria and Ponyville.
A Sinister Stallion: Clearwin spots an elusive figure.
Rarity's Sorrow: Rarity and Rainbow's theme.
Nightmares From the Past: Autons, Daleks and more.
Winter Queen Zima: Zima's theme.

I must say it is unlikely this story will ever finish due to not liking how it would play out. However, you can still see what was planned below.

The next chapter shows that Cloudsdale is now covered in boards and blimps to give Unicorns and Earth Ponies a way to live there. Twilight meets with Celestia, Luna, Spitfire, Gilda, and Lightning Dust to say that Rainbow and Rarity are missing and they need Rainbow for their plan to remove the cloudcover over Canterlot to burn Zima out. Twilight is uneasy about the plan since she had seen a Dark One burn up in sunlight before and can't bear doing that on purpose, but Celestia tells her it's the only way.

At Canterlot "Mr Pepper" advances on Rainbow, Clearwin, and the Doctor, but stops when it receives orders from Zima on how Clearwin and the Doctor cannot be harmed. The Doctor senses something off, and then many more monsters he is familiar with—Sontarans, Cybermen, Zygons, Silurians, Ice Warriors, and more—pour in to take them back to Zima. He knows them working together is extremely unlikely and demands to know what's really happening. Finally he asks if Blackmirror is there, and the monsters stop, their eyes turning purple, speaking as one to inform the Doctor that the monsters are merely psychic projections called Dreamspawn. The Dreamspawn army introduces itself as Blackmirror and informs them that it is responsible for bringing the Doctor to Equestria. It has already promised Zima can keep Clearwin but it wants the Doctor, telling him to come inside the TARDIS and meet the true Blackmirror at the Eye of Harmony. The palace is then attacked by Celestia's resistance, forcing the Dreamspawn to defend the Dark Ones. Rainbow escapes to join the attack, and the Doctor goes back into the TARDIS with Clearwin to find the Eye of Harmony, a room where the TARDIS' true power can be regulated. The living darkness inside peels away for them to journey deep inside, the Doctor asking about cutie marks and Clearwin asking about the Doctor's home. The Doctor tells her of a place called Gallifrey but it was destroyed by the Daleks long ago. Clearwin again sees the evil-looking old stallion lurking around, but he vanishes before the Doctor can see. They arrive at the Eye of Harmony where a group of Dreamspawn Weeping Angels stand guard as the living darkness swirls around the Eye as Blackmirror slowly crawls out.

Above the palace a swarm of flying creatures including Pegasi, Griffins, and Dragons are swirling around in the air, eroding the magical clouds while Earth Ponies and Unicorns attack from the ground. The Dreamspawn army greatly bolsters the Dark Ones' forces though, and Celestia's forces are completely unprepared for their power. Mr Pepper alone kills many of the flyers but the clouds begin to break up. Inside Rainbow is attacked by a feral Dark One Rarity but when Rarity is about to kill Rainbow she suddenly darts away and pulls a curtain open, exposing herself and many Dark Ones to the new sunlight. The Dark Ones retreat while Rainbow takes a severely burned Rarity out. The Dark Ones hole up in a safe dark place except for the Heart Sisters who lead the Dreamspawn army.

At the Eye of Harmony Blackmirror gloats that the Doctor made it possible for her to escape her prison as the Angels block the Doctor and Clearwin from leaving. Blackmirror tells the Doctor his tortured psychic energy will create an endless army for Zima to make her conquest of the other Equestria effortless. The Doctor figures out that his arrival broke a fixed moment in time, an event that if changed by time travel will have catastrophic consequences, and that there must be two Equestrian timelines. Blackmirror confirms this, saying that this timeline is decaying and the normal timeline where Ice Draught was destroyed by Sombra is still fresh and full of life; it will be Zima's reward for serving her to have a new land to ravage and enslave , and Blackmirror is casting it into eternal darkness as they speak. Blackmirror points out that the Doctor made all of this possible. Clearwin asks how, and over the Doctor's protests Blackmirror shows moments from the Doctor's life, that he had traveled back to kill the Daleks before they had a chance to be dangerous which started the war between them and Gallifrey, and then that it wasn't the Daleks who destroyed Gallifrey but the Doctor himself. Clearwin is horrified and the Doctor yells at her how both sides had to die to spare primitive places like Gallifrey the horrors of that war, but he breaks down in guilt, admitted he hated himself so much for killing his people. Blackmirror explains that during the war time and space became so damaged that she was able to send a piece of herself out of her prison that attached to the TARDIS, growing in power with the Doctor's grief and rage, the breaking point coming when the Doctor's last companion's died. The living darkness possessed the Doctor during his nightmares, making him enter Equestria and destroying the TARDIS console after to engineer breaking the fixed point in time. Feeling defeated, the Doctor sinks into despair over how he had been used as more Dreamspawn grow from his psychic energy, Blackmirror telling him that she will take all his bad memories away so he can be at peace. Clearwin reminds him of the good things he did though, that surely he was making up for Gallifrey's destruction by helping people. Inspired, the Doctor realizes that for all the bad memories he has he made many more good ones and that those memories are so good because of the bad. The Dreamspawn dissolve into golden energy that the Doctor destroying the living darkness with, cutting the incomplete Blackmirror in half before absorbing the memories again. Blackmirror curses the Doctor as she breaks into glass, telling him that as he lies dying on the fields of Trenzalore to remember that she offered him peace.

Outside the Dreamspawn all vanish, leaving Celestia's forces to attack with everything they have. The Heart Sisters panic and start to use The Way of Blackmirror to leave for the other Equestria early, the evil power of the book teleporting the Dark Ones away to the time vortex to travel to the normal Equestria. Rainbow and Rarity watch, wondering what will happen next.

The living darkness gone, the TARDIS begins to repair itself violently. The Doctor, in pain after all the bad memories returned, swoons and Clearwin is forced to carry him back to the console. The mysterious elderly stallion shows up though, cursing Blackmirror for not being able to kill the Doctor. Clearwin begs the stallion to leave them alone, but the stallion says the Doctor must suffer for his crimes and that Clearwin is an abomination, always getting in his way. He viciously stabs Clearwin with his horn and icy magic, but the TARDIS crushes the stallion by shutting a heavy door on him. The Doctor wakes up and bandages Clearwin, saying he must fix the fixed point in time then stop the Dark Ones before they ruin the other Equestria. Clearwin realizes that she is the fixed point in time, that she was supposed to die when Sombra caught her. The Doctor refuses to take her back to die, but Clearwin insists it must be done. Reluctantly, he sends her back where Plough Drag cuts her with his scythe, leaving with Sombra to begin the revolution. The Doctor stays with the dying Clearwin, but she urges him to stop Zima. He leaves and she whispers "Run you clever boy...and...remember..."

Rainbow and Rarity find themselves fading away. Rainbow is scared but Rarity thinks that things will be better for them. The false Equestria crumbles away, replaced by the real one where Celestia is still in charge.

Zima rages that she doesn't have Clearwin like Blackmirror promised and the other Equestria will suffer for it. They stop in the vortex and the Doctor appears, letting them know he tore pages out of The Way of Blackmirror so they are now stuck forever. He leaves and the Heart Sisters take the book and try to escape the vortex to save Zima later, taking them to Sombra as he is destroying Ice Drought. He kills them and takes the book.

The Doctor arrives in the normal Equestria, right after The Magic and the Night ended, asking about Ice Draught. He is directed to the far north where he finds the ruins of a town. Sad, he leaves a small memorial to Clearwin, and leaves Equestria, becoming a Time Lord again. Angry and bitter, he feels sick of adventure and decides to settle down, wondering how Vastra and her friends are doing.

As he leaves, The Way of Blackmirror appears over the ruined town, casting a spell on its own. The Heart Sisters' ruined corpses rise up like at the end of The Magic and the Night, vowing that they will bring Ice Draught and Zima back with Blackmirror's power.