On a calm relaxing morning in Canterlot, the Mane 6 were outside the castle and enjoying the sunlight, and having a picnic together. As for Rainbow Dash, she was sitting on her lounge chair with her sunglasses on and getting some heat from the sun. “Ahh... nice day, huh?” Rainbow Dash asked. “Indeed, darling. It is such an amazingly beautiful day outside,” Rarity replied. “Yes, but have any of you seen my baby?” Fluttershy asked. “Yeah, where is the little feller?” Applejack asked.
“Momma! MOMMA!!” Thomas screamed. “Oh my! That sounded like little Thomas! It’s like he could be in big danger!” Rarity said. They then saw Thomas screaming and running over to his aunties. “Thomas, what’s happened?!” Twilight asked. “I found him in the restricted section,” Sunburst said. “But we’ve got him out in time,” Starlight said. “What’s wrong?” Fluttershy asked. “You’ve got to see what happened!” Thomas replied, pointing at the sky turning dark, until they saw a blackish misty fog surrounding them, until a huge black inky cloud appeared and transformed into a giant shadowy alicorn stallion with while glowing eyes and a jagged mouth, and its mane flowed like Celestia’s and Luna’s, and its wings were as wide and sharp as a metallic bird.
“The Pony of Shadows?! But how?!” Twilight asked.
The Pony of Shadows then let out an evil cackle, and then looked at the group of ponies that stood in front of him. “After all these years, I’m finally free! And I can finally have my revenge!”
“This is impossible! How did you appear?!” Sunburst asked.
“Well, I have that apelike creature there to thank!” The Pony of Shadows replied, pointing at Thomas, who was being shielded by Fluttershy.
“It’s not my fault! It was an accident!” Thomas said.
“Of course it was! And now that the pillars aren’t here to stop me, I can finally spread this world with eternal darkness forever!” The Pony of Shadows said, and then flew off with a puff of smoke.
“Auntie Twilight, I... I-I-I... I did-didn’t mean to,” Thomas said, until Starlight walked over to give her nephew a hug against her chest. “Shhhhhh... It’s not your fault, sweetie. And don’t worry. We’ll stop this. But we better find out what’s really going on,” Starlight said, until she gave him a kiss on the forehead. “I’m sure Princess Celestia will know what’s happening,” Twilight said. Thomas nodded, and then they went over to the castle.
“The best elements within us can spread light and virtue, and I know ponies who represent them all – strength, bravery, healing, beauty, hope, and sorcery. Myself and these Pillars of Equestria were gathered together by another to maintain and share the light of these powerful ideals. But we soon came to believe the pony who brought us together only wanted that power for himself. Cast out and alone, this power-mad pony turned to darkness to satisfy his thirst. Transformed into a Pony of Shadows, he returned for revenge – to extinguish the Pillars' light and rob the world of hope. To stop him, the Pillars and I must make a grave sacrifice. But we shall leave behind a seed in hopes that one day it will grow into a force to stand against the darkness for all time. We must now face the fiend with the only plan we have...”
"...I only hope it will be enough." Sunburst finished narrating. “That's the last entry. And maybe Starswirl's final words before he vanished.” They all gasped, including Thomas as he hid underneath his mother and hugged her leg while nuzzling with her fur with tears in his eyes.
“I've always wondered what happened to Starswirl. This is quite a discovery, Sunburst,” Princess Celestia said. “So it's genuine? You can verify that this journal really belonged to Starswirl the Bearded?!” Twilight exclaimed. “Indeed. From the looks of it, the last thing he wrote before facing the Pony of Shadows,” Princess Luna replied. “Uh... So, the Pony of Shadows was really real?” Rainbow Dash asked.
“It appears so,” Princess Celestia replied. Thomas shook nervously and softly whimpered, until Fluttershy placed her wing over him. “We never met the other Pillars, and we were too young to understand the danger they faced,” Princess Luna said. “Hold on a second now. All those legendary ponies were real, too? And they went off with Starswirl to face the Pony of Shadows, and then none of them were ever heard from again?” Applejack asked. “Uh, yeah. Weren't you listening?” Pinkie Pie asked in reply.
“But w-wh-w-what happened to them all?” Thomas asked nervously. “They must have defeated the villain, since Equestria is still full of light and hope,” Rarity replied, stroking her nephew’s hair softly. “But how? And where did they go?” Starlight asked. “My Olde Ponish is a bit rusty, but I wonder if the answers can be found somewhere within the pages of this book,” Princess Celestia said. “Well, I just happen to be an expert in Olde Ponish. I mean, I've practically memorized every ancient text about Starswirl there is!” Twilight said. “Seriously. All of them,” Spike said. “We have fond memories of our old teacher,” Princess Luna said. “If you could discover what happened to him, we would be most grateful.”
“Solving a thousands-year-old mystery could take forever!” Sunburst said. “Think of the research! The re-reading! The re-re-reading!”
“You might find you need help,” Princess Celestia said. “Luckily, she's got a whole bushel o' helpers right here,” Applejack said. “Totally!” Rainbow Dash said. “Uh... how long will all this research take, Momma?” Thomas asked. “I don’t know, sweetie. But don’t worry, I’m sure we’ll find a way to end it soon,” Fluttershy replied as she hugged her son closer to her chest, and then kissed him on the forehead. “Let's get this back to my library. I'm sure we'll figure out what happened in no time,” Twilight said, and after Fluttershy placed Thomas onto her back, the rest of the Mane 6, including Starlight and Sunburst walked out of the castle to head back to Ponyville with excited chatter.