It had been seventeen years since Pinkie Pie's death, and everything had returned to normal. Rainbow Dash had retired from the Wonderbolts, Applejack was living comfortably with her family, Rarity and her daughter had returned to their shops in Canterlot and Ponyville respectively, Fluttershy still lived in her cottage by Everfree forest tending to the animals, and Twilight had graduated with half a dozen degrees under her belt and was now a teacher of magic.
Twilight Sparkle was teaching a class at the school at Canterlot for Gifted Unicorns when Rainbow Dash barged in, panting. Setting the chalk down, she walked over to her friend. "What is…"
"Fluttershy's gone missing!" Dash blurted out, clearly shaken.
Twilight's eyes became pinpricks before she announced "That will be all for class today."
As the students shuffled out, Twilight led Dash to the front of the classroom. Twilight noticed she looked exhausted. "Tell me what's going on," Twilight admonished.
"I went to see Fluttershy at her cottage because she hadn't been seen in town for a few days, but when I got there the door was opened and… and I looked all around until I found a note, and the note said that she was going to Zecora's, and…"
"Rainbow Dash, breathe," Twilight ordered her friend.
After a few seconds of hyperventilating, Dash took in large gulps of air. "We need your magic to help search for her," Dash finally got out.
Twilight nodded, frowning. She knew time was important when a pony went missing, so she left a quick note that she taped to the door saying there would be no more classes for the day. After picking up Rarity, there was a quick ride on a Pegasus chariot, taking them to Ponyville. Since Ponyville's library was run by someone that thought silence was necessary in a library, they decided to meet at Sweet Apple Acres with Applejack.
"I must say, Twilight, you look absolutely stunning. What do you do to keep that youthful look?" Rarity asked with a twinge of jealousy.
"The same thing I told you when we met at Canterlot," answered Twilight.
"Oh, of course," came Rarity's quick reply. Silence fell on the group. "So why are we here again?" asked Rarity.
Twilight and Dash looked at her flatly before Twilight responded, "We're trying to find Fluttershy, like we told you on the chariot."
"Oh yes, quite. How silly of me," was Rarity's quick response.
Dash and Twilight looked at each other, worry in their eyes.
"Are you feeling alright, Rarity?" Twilight asked hesitantly.
"Never better," was her curt response.
The rest of the journey passed in silence.
When they arrived, they saw Applejack playing with some fillies and colts, most likely her grandchildren. At the grave look on her friends' faces, she brought playtime to an abrupt halt and went with them inside a barn.
"So what's with the long faces?" Applejack asked, trying to inject some levity in her friends.
"Fluttershy's gone missing," was Rainbow Dash's morose response.
"Oh my stars!" AJ gasped out. "Did-did you check her cottage?"
"Yes, but I only found this," Dash said, pulling out a hastily-written note out.
Twilight took it in her magic and set it before her face and read aloud, "'Going to Zecora, will see you all later.'"
Applejack gulped. "You mean to tell me she went into the Everfree Forest alone? She-she should have called me, called somepony, to go with her. It ain't safe to go alone in there."
"I must say, surely Zecora could have looked after Fluttershy just fine. After all, she lives there," Rarity stated.
"Rarity, Zecora's been dead for five years," was Applejack's flat reply.
"Oh, of-of course. How silly of me," she laughed half-heartedly.
Something was niggling at Twilight. She read and re-read the note, feeling something important was there.
"Wellp, better get a search party set up. I know fer sure that the Apple family would be happy to help," Applejack stated.
"I'm helping, too! No way am I leaving Fluttershy alone there," Dash assured.
"My magic can help find Fluttershy in a jiffy," Twilight smiled. As long as she is alive, she thought.
"I'll get the rescue party set up," Rarity said, leaving the barn.
They quickly set up the search effort, with Rainbow Dash leading a party through Everfree Forest despite her friends' wishes. Twilight tried every locator spell she could find and remember, and a few she made up on the spot; none of them found her. This discouraged Twilight more than the search party's lack of success. She voiced her worries to her friends that night: "I don't think we'll find Fluttershy alive, if at all."
Silence greeted her. She didn't want to say it, but she had to state the reality of the situation.
Rainbow dash was the first to speak. "You don't honestly think that, do you?" when Twilight didn't meet her gaze, she was crestfallen. "You do. Well, I won't give up on my friend! I'll go out there by myself if I have to!"
"Dash, how long has Fluttershy been gone?" Twilight asked quietly.
Rainbow Dash started to tear up. "I-I don't-"
"When was the last time anypony saw her?" Twilight continued in the same quiet manner.
Dash dropped to the ground, hooves over her eyes. Twilight walked over and put a hoof on her back, trying to comfort her.
"I promised to protect her. I promised to look out for her. I promised…" Rainbow Dash croaked out.
Twilight sent a letter to Celestia telling her that she wouldn't be able to teach for a week. If they hadn't found found her by then, they probably wouldn't.
Repeated combing of the forest proved dangerous. There was one encounter with a cockatrice and another run-in with a hydra. Luckily nobody was permanently injured.
A week came and went and no trace of Fluttershy was found. Rainbow Dash was taking her loss the hardest, blaming herself. Memorial services were quickly scheduled after the week was over. When Rainbow Dash tried to give a toast, she broke down in tears. Rarity seemed to forget what she was doing halfway through, making Twilight worry about her. Applejack gave a great talk that left everyone crying. Twilight just said how kind Fluttershy was, and how good a friend she was.
After the service, Twilight took the train to Canterlot, brooding. She was disappointed in herself for not finding at least the body. She had lived at her cottage, alone with her animals. Thinking back to the note, she came to the horrifying realisation.
"'Going to Zecora,' not 'going to Zecora's.' She knew… oh by Celestia, she knew…" she couldn't make her mouth say the words, but that didn't matter. Fluttershy knew she was going to die! That thought chilled her, a thousand thoughts running through her mind. She was in a daze when it came to the Canterlot stop.