This one (of the) time(s), at CSGU
Twilight and her friends waved as Princess Celestia left the library and joined the royal guards outside. Some of whom were looking rather sheepish at not arriving in time to help earlier, leaving Twilight and her friends to once again protect everypony.
With Celestia off, Applejack spoke up. "Well I need to get going y'all. This has been one hay of a day and I still got a farm to take care of tomorrow."
"Oh my yes, look at the time!" Rarity exclaimed. "It would be best if I turn in as well."
The others agreed it was time to leave. They were tired before the 'We saved Ponyville, again. (and Twilight is secretly an alicorn.)' party and some of them were even taking short naps while it was going on.
Twilight waved as her friends left but noticed that one had stayed behind. Turning around she saw Rainbow Dash watching the others leave. She closed the door and walked over to her remaining friend. "Was there something else?"
"Yeah." She took another glance at the door. "I wanted to ask you about something."
Twilight held up a hoof to stop her. "I know you're excited about the idea of me going flying with you, but you will just have to wait. I don't know when they'll start growing but it'll be soon. Within a decade at the latest." She felt some tingling in her back. "Probably a lot sooner."
"That's not soon to most ponies." Dash grumbled to herself. She shook her head. "No, that's not what I wanted to ask. You said that what happened was no big deal because you died before and there were parts missing."
Twilight blinked at her a couple times. "Well... It was unpleasant but yes I have died several times before. And no there's nothing missing. I've lost a few pieces at times but everything grows back."
Dash tilted her head to the side. "But I thought you said there was part of your skull stuck in a wall?"
It took Twilight's tired mind a moment to remember everything she had said earlier. "Oh that." She frowned at her friend. "Are you sure you want to know about that?"
"It's why I waited until Fluttershy left."
Twilight hummed and tapped her chin. "Ok then. It was actually the first time the princess was teaching me how to...
Celestia smiled at her prized pupil as she watched some of the wisps of magic coming off of Twilight's horn shift from their normal hue to a bubbling green and black.
Despite her chronological age compared to other ponies, Twilight was still a filly and as such still had the expected wide eyed excitement upon hearing what she would be learning today.
The wards around the classroom would not only stop anything dangerous from getting out, but would also prevent anypony outside from wondering how a unicorn filly was learning how to channel alicorn magic.
Celestia had been giving Twilight and Shining Armor private lessons for years. But with Shining rising through the ranks of the royal guard and Twilight pulling off a feat that let Celestia take her on as a personal protégé, it was so much easier to get time alone with one of them in a secured area.
"Ok, Twilight. That should be good. Now channel it into the gem and let's see how you did." She pointed a hoof at the large gem sitting in a small wire stand between them. "...Twilight?"
Twilight's face was scrunched up with her eyes closed and her ears pinned back. She was quietly muttering the lesson over again to herself.
Celestia could tell what was happening and reached out with a hoof. "Twilight!" At Celestia's touch, everything went wrong. Twilight's concentration was broken and the magic she had been building up was released without control or direction.
Twilight's head exploded in a blast of magic and brain matter. The shockwave tore apart her chest and sent her fore legs flying against opposite walls while her torso slid backwards across the floor and toppled over.
Celestia was picked off the floor and sprayed with bone shrapnel. She slammed into the wall and that's where she stayed.
Twilight's hind legs were kicking, spreading what was left of her around in circles. Celestia twitched and jiggled a little from her spot on the wall. Outside the door all that was heard was a light pop and a slight shake. A quick check confirmed that the door was still locked and secured.
For several minutes the room was quiet as the two dead ponies bled on the floor.
...
Celestia blinked a few times and looked around but her eyes wouldn't focus on anything. Trying to turn her head proved futile, as the most that would do was turn her body a little. Using her magic, she felt around and found the problem. She pulled the intrusion out of her head, through her face, and promptly fell to the floor.
She sat up and waited for the hole through her head to close up and her eyes to realign. Once she could see straight, she looked down at the purple horn she held in her magic. She placed it where Twilight had been and then dragged her torso and fore legs over.
Celestia calmly picked pieces of Twilight out of her own body and dropped them into the pile. The process was occasionally interrupted by a wet squishing and slapping sound causing her to look over and see something flopping around in the gore as it reattached to the reforming body.
Tendrils of tissue slithered through the mess, growing larger as they collected more material. Muscle, bone and sinew formed the framework, before the liquefied organs flowed into place and took shape. Her fore legs were reconnected by the time her spine had reformed up to where the base of her skull would be. Her spinal cord went past the jigsaw puzzle that was her skull and started rebuilding her brain as it reached for her horn.
By the time Celestia was done, Twilight's mostly reattached horn was pulling lost pieces into place while the last bits of blood trickled back into her. Twilight moaned as she sat up. Her skin was still working its way up her neck, leaving her eyes exposed as they rolled around in their sockets while Twilight fought to regain focus.
Celestia went over the room with her magic, using a touch up spell that would quickly fix most of the damage. She waited until Twilight's skin and fur had finished regrowing. "Feeling better?"
Twilight rubbed her head and whimpered. "My whole body has a hornache."
Celestia nodded. "You did use a lot of magic."
Twilight kept rubbing at a spot on top of her head next to her mane.
"Did you learn what went wrong so you can avoid it happening next time?"
"Yes, Princess." She answered but didn't leave her head alone.
Celestia frowned and leaned closer. "Twilight, is something wrong?"
"It feels funny. Like something's missing."
Her horn lit up as she reached out with her magic. "Yes, there is a piece missing. Can you sense where it is?"
Twilight shook her head and then winced.
"Hmm..." Celesia kept checking with her magic. "It's ok, it's already starting to regrow. Latter I'll teach you a spell that will make it easier to find things next time this happens."
Twilight lowered her head and looked up at Celestia. "I'm sorry, Princess."
She looked down with her eternal smile. "Whatever for?"
Twilight pulled in on herself and looked at the floor. "I was so excited about todays lesson, and I tried so hard. You were going to teach me something special. And I failed."
Celestia quietly laughed as she stretched out a wing and placed it on Twilight's back. "It's ok, Twilight. Remember, we're still just ponies and all ponies make mistakes"
She thought about it for a moment. "Even you? But-but you're the princess!"
She hesitated for a moment. "Even me." She stood up and lifted Twilight onto her hooves. She ended her personal wards as she opened the door and picked up the discarded gem.
They left the room together, with Twilight by her side as they walked down the hall. "Don't worry about today's lesson, Twilight. I know you tried hard and I knew it was going to be difficult. You did very well for your first attempt. We'll try again next time."
Twilight looked up at her with a smile. "Really?"
Celestia nodded. "After you've had a chance to properly recover from this." Then she gave her a push with a wing. "Now go get something to eat and get some rest. You have a lesson on blood magic after lunch."
Rainbow Dash blinked at her. "So you not only killed yourself, but took out Celestia as well, and nailed her body to a wall?"
Twilight looked off to the side. "Well, I wasn't exactly 'there' at the time but that's what she said happened." She watched Dash yawn and her eyes seemed to droop a little more. "You really should get going while you still can."
"Yeah, yeah." She made her way out the door. "See you later, Scrambled."
Her eyes narrowed. "Scrambled?"
"Yeah. I'm still calling you egghead." Dash jumped into the air and started flying away.
"Hey!" Twilight yelled out, but it was too late.