Takes place during Part 2 - Chapter 3...
After Xehanort witnessed the vines disappearing in several rainbow lights, he sneered as he felt everything has gone according to plan; Sora came to Equestria and saved the day, just as he always did for every other world.
"And now, the stage is set...all I need to do at this point...is simply retrieve my 13th Darkness."
Xehanort walked down the stairs back into the ravine and made his way to the cavern with its current inhabitants unaware of what's coming before them...