YO! 1000+ upvotes?!
It cannot be, oh my gosh! You mad lads!!!

1. Twilight and Princess Luna investigate why every unicorn whose magic specializes in time travel mysteriously goes missing.  
2. On their way back to Equestria from one of their travels, they find out the answer: everypony who travels through the times between time eventually gets an urgent message of “The Princess is dying: send immediate aid” followed by a spell on how to teleport to totally bizarre coordinates  
3. They waste no time teleporting to rescue Celestia.  
4. JK, it was in invitation to Luna’s demise at the hooves of the Nightmare (which is the same corrupting entity as the Pony of Shadows in this story). Luna immediately returns to Canterlot to let Celestia know that the message that time travelers eventually receive is for her death sometime in Equestria’s future and not a current threat to either Princess. Twilight, however, is trapped with the rest of the time-traveling ponies. The original draft had Luna teleport directly into her demise like a trap, rather than witness her future self and the Nightmare destroy each other. I changed it when I moved from branching timelines to stable time loops and that required Luna to be there twice.  
5. A while later (between 2 weeks and 20 years, still working on the exact timelines), Shadow Princess Twilight returns and banishes Luna to her grand exit scene.  
6. Princess Celestia just witnessed her sister, who she had waited 1,000 years to return and looked forward to ruling together for another thousand, get yote within 20 years of her return by a malevolent entity who dared to use a corrupted likeness of one of her many faithful students who tragically vanished. She does not engage any of the usual self-preserving power regulation (in my story, very bad things happen to a unicorn who severely overdrafts her magic).  
7. After she had her unlimited power (if only for 30 seconds), the reality that both Luna and Twilight are gone gone hits her and she is catatonically depressed for the rest of the story. Cadence takes over the day-to-day duties of governing Equestria until Flurry Heart is old enough to be Celestia’s body double for PR duties.
    
   If this sounds way too complicated, you’re absolutely correct. Don’t try to devise plotlines involving multiple time travelers and attempt to keep any internal consistency to your story.

Have a Snickers bar Tia, you’re not you when you’re hungry.