On seeing a link from Reddit, [link], I have concluded that Discord is the TARDIS's consciousness in Equestria.
If you can piece together that the *Tree of Harmony is the same thing as the **TARDIS ARS, we can conclude that the entirety of the FIM universe is a pocket universe created for the enjoyment of the TARDIS whenever the Doctor is off being... Doctory. (Or if it's a remnant of a long destroyed TARDIS)
Now, the TARDIS ARS is fully capable of doing that which Discord and the Tree of Harmony can do--as far as I am aware--and this is the TARDIS we're talking about.
Why. The hay. Not.
My Little Pony: Friendship is Magic is a pocket dimension which uses the TARDIS ARS room, which the TARDIS enjoys by manifesting itsself as Discord and... "watching the show."
- or -
The (a?) TARDIS crash landed on this planet, and the ARS room is the Tree of Harmony, while Discord is the soul of the TARDIS.
Discord is an observer from the outside.
It's all a show made by the TARDIS, for the TARDIS.
From the FIM universe, it's the thing in control of all growing things or something.
** TARDIS ARS -
As ponyriv puts it from reddit,
'That's the 'TARDIS Architectural Reconfiguration System'. It's described as "living metal, capable of rearranging particles to provide the user with whatever he needs, and worth more than the combined value of all money in the universe." '