It had been three weeks since Twilight Sparkle was put into a coma. Spike and Rainbow visited and brought gifts in hope that she would wake up every day. One day they both went together, only to be stopped by a doctor pony.

"Rainbow Dash, Spike...I have some bad news..."

"Wha...what is it, doc?" asked Rainbow.

"Twilight Sparkle's examination is over. The other doctors estimate she has about an hour left to live."

Rainbow looked over at Spike. His mouth was open, but no words came out. Tears were flooding down his cheeks. Rainbow reached over and pulled him close. "Shh, Spike. It's okay." But even she felt it wasn't okay. She was going to lose her best friend. The two cried as they walked into Twilight's room. She had awakened from her coma, but soon would be asleep once more.
"Twi..."
"Rainbow. You came to visit. How nice. I like the gifts you and Spike brought me. They're nice."
Spike couldn't take it. He ran and jumped up next to Twilight, thankfully not damaging her delicate body. He hugged her and soaked her in tears.
"Spike...you'll be okay."
"No, Twilight. I'll never be okay. Not without you!"
Twilight held him close and signaled for Rainbow to come over. She whispered in Rainbow's ear:

"Take care of him. I put my trust in you, Dash."
Rainbow stared at Spike and Twilight.
"Okay...for you." She said as she took Spike in her arms. The two stayed with her until her time was almost up.
A doctor walked in the room.
"Rainbow, you need to leave now."
She looked one last time at Twilight. It was clear she was in pain. Her eyes were halfway closed. She was no longer able to speak.

She walked over, placing a hand on her hand.
"No, doc. I'm staying here with Spike until the end. I'm not leaving my friend here to die alone."
The doctor left, not wishing to get involved.
Twilight's eyes were closing. Her life was ending. Spike couldn't watch.
"I...I'll miss you, Twi..." Twilight managed a smile.
Then it was all over. No more pain.
Twilight was gone.

Epilogue

Twilight Sparkle's funeral was held two weeks after her death. Not a single person's face was dry at the funeral. She looked so peaceful in her grave.

Ponyville was never the same after that. The weeks following were like a normal town, but every time the date of her death passed almost not a word was spoken.
Spike lived with Rainbow Dash, and Rainbow barely flied anymore. She spent all of her time with Spike.

Applejack went on living a normal life, bucking apples and such but felt a gaping hole in her heart.

Rarity designed dresses for all the ponies for things like the Gala, and always made one extra. It made her feel better to know that she had dresses for Twilight. Others in town thought she was crazy, but her friends understood.

Pinkie Pie was changed the most. She wasn't her party animal self for quite a while. She often sat outside just staring off into the distance.

Fluttershy cried for almost a week. She could not abandon her animal caretaking duties, so she forced herself to be tough.

One day, Princess Celestia was seen at what was left of Twilight's house. She left a flower and a letter in her mailbox.

The letter was never to be read by anyone.

"My dearest Twilight Sparkle,

You were my most faithful student. No others could compare to you. I hope you read this from heaven and know I remember all of your progress in life. From stopping Nightmare Moon, to defeating Discord, all the way up until now.
Goodbye, Twilight.

~Celestia"