I remembered there was something named "the child of nightmare" mentioned in the time war, and I got an idea.

So.... this is the prologue

The Nightmare was that entity. It runaway from the center of warzone and landed on Equestria.

Nightmare, just like most doctor who villains, was an entity that incapable of feeling some emotion that humans and ponies could, such as empathy, love, etc.

Nightmare took over Luna's body, fought against celestia, got rainbow laser on the face.

But the element not only banished them to the moon, it also harmonized them too.

Mental barrier between two mind collapsed, and a new being was born. Not quite the Nightmare or Luna but also both at the same time.

A brain made from symbiotic relationship of otherworldly creature and night princess, capable of comprehension concept beyond pony's brain could and capable of emotions and the way of thinking that only meaty creature could experienced.

This new creature would adopted the name that led to her birth, one that contained both of her root, Nightmare Moon,

Now it's time for her adventure! maybe there was a broken tardis on the moon? Maybe the doctor suddenly appear? Maybe she served her sentence and runaway to the edge of the world and found a tardis in her journey.

I imagined her character to be a not-coward version of discord whoove. Knowledgeable and brave, but not as kind-heart as the doctor and willingly to kills. Her Luna side would sometimes forced her to protect the weak but she would be ruthless and pragmatic about it.

Give her a companion or two too.

My recommendation lists
1. Pre-returned starswirl - the ruthless hero of ancient equestria that was also a great scientist.
2. Twilight clone - young but resourceful mage who always made Starswirl’s eyes twitched with her modern magic theories.
3. Iron Will - Highly intelligent scammer that looked like mindless brute at first glance. His acting skills could fool the cyberponies.