Immediately after returning the defeated Alternate Timeline villains to their right timelines AND helping the locals of those alternate timelines adjust to no longer being under the control of villains (to say nothing of also equipping and training the locals in the alternate timelines to be better able to handle other villains in the future), Doctor Whooves and the Mane Six start for home in TARDIS. However, on the way home, the seven of them actually come across a time line where, even though the Sonic Rainboom never happened, things are actually no worse than their own timeline. Sure, there is a different set of Element Bearers in this time line, but things are actually running smoothly all things considered.