Inspired by the prequal to the Dr Who 50th aniversary special, the short showed Paul McGann's doctor choosing to become a warrior to fight in the Time War, introducing John Hurts 'War Doctor' with the phrase "Doctor no more..."
In the slice of life episode (forgets actual title and ep number) Dr Whooves aludes to the time war in a round-about way, though obviously I doubt Hasbro could go all the way with the crossover for the time being.

The above scene shows Dr Whooves return to Gallifrey at the peak of the Time War, only to find that the home that had shunned him for so long was in dire straights. Even if they had exiled him for his escapades, they were his people and his home.
As per the prequal, he regenerates and abandons the Doctor title, which is starting here.

After setting this scene up, barring the extraordinary rendering time (36min for this one shot) I might just make an animation with it. Something along the lines of what I think a Dr Whooves based episode (based on the aniversary ep) could look like. Plus, if he dragged the mane 6 along, I could get into applejack bucking daleks left right and centre.

Dr Whooves model by
Dalek models by Zagony & Benjee10 on BlendSwap.
Tardis by (sorry, I can't remember where I got it or who it was by, they made an awesome model though)
Timelord citadel and landscape made by me.

All things portrayed here remain property of their respective copyright holders, I make no intention of getting any financial gain from any use of these materials.