Thanks to Pinkie Pie, Twilight Sparkle had learned to not get bent out of shape when she came across something that was too nonsensical for her to comprehend. A lot of aspects regarding the process that produced zap apple jam were exactly that, so she had put them out of her mind and focused on the things that might actually be explainable, and thus rewarding should she figure them out.
One such aspect, seemingly minor in the grand scheme of things, were the timberwolves who howled when the apples of the zap apple tree began to grow, which was rather curious. There was no record of them doing that for anything else, that she could find, and that made her wonder why such a relationship existed.
Further research into timberwolves didn't yield much, beyond producing more questions than answers. Despite their fearsome portrayal, for instance, she couldn't find a single pony fatality attributed to them. Also, it was strange for an assumed predator to have really bad breath as a part of their nature, which would alert prey to their presence — it was usually the prey animals that used offensive smells, in order to ward off predators. And what could timberwolves be prey to, either because they were made of tree parts or because they could break into pieces and reassemble themselves?
It proved to be very intriguing, so she had decided to disguise herself as a timberwolf, in the hope of being able to mingle with them and learn more. Her friends had been worried, of course, but she had assured them that she would teleport herself to safety at the first sign of trouble, and that she would be back before sunset. If they didn't see her by that time, then they could worry that something was wrong and it would be alright to interrupt her investigation even if everything turned out to be alright.
Once she had traveled far enough into the Everfree forest to lose sight of her friends, she paused to check her disguise one more time before steeling herself and continuing onward, hoping that the hollow bough that hid her horn would have the desired effect since timberwolves didn't have such a protrusion. She stuck close to the edge of the forest, where it met the Apple's orchard and the zap apple trees, and did her best to avoid the undergrowth because she didn't want a part of her disguise to get snagged on something.
Sooner than she would have expected, her nose caught the tale-tell sign that a timberwolf was nearby, prompting her to stop moving and look around herself warily. She quickly turned to face a nearby bush when it rustled, and a second later a timberwolf stepped out of it, who stopped and regarded her for a moment before approaching her cautiously. As it did, she gulped and tried to stay calm while she held her ground, hoping that her legs would work if she had to move.
The timberwolf leaned in and sniffed about her head, which she drew back a bit before she caught herself. She only just began to notice that its breath was no longer foul when she saw its face lighten up and its tail wag, which she assumed was a good thing, before it turned about and left the way that it had come.
After releasing a sigh of relief, she levitated a pendant from behind the plank of wood that covered her breast and hung it on a tree branch, so she would be able to home in on it later and find her way back to the edge of the forest. With that done, she hurried around the bush to follow the timberwolf, her nervousness giving way to excitement.
If the timberwolf minded that she was following it, it didn't show it. In fact, unless she was mistaken, its gait seemed to have a bounce to it. She followed it to a clearing, where five other timberwolves were lying down, whose heads perked up upon their arrival. Their gazes locked onto her immediately, and the spike of fear that was triggered by the attention almost stopped her in her tracks, but she soldiered on and slowed down instead.
She did stop, however, when the timberwolves got up and approached her while the one that she had followed sat on its haunches and watched. Like her last meeting with a timberwolf, these also investigated her with their noses, and she could feel sweat drip down her brow while they checked her out, due to effectively being surrounded by them.
Much to her relief, they appeared to accept her as the first one had, only this time they turned playful and seemed intent on playing a game. Said game began when the first timberwolf barked a challenge and the others gave chase, which she was reluctant to join because of two closely-tied problems: risking discovery if she were caught with too much force, or from running and using her magic to keep pieces of her disguise from jostling off. Since it might be suspicious if she didn't play with them, though, she set her jaw and braved the trial ahead of her.
The next few hours of chasing each other around and hiding in the woods were hard and draining, but she somehow managed to get through it all without revealing herself, albeit with a couple of close calls. Thankfully, the timberwolves decided to take a break before she collapsed, and hid her delight when she returned to the clearing and laid down with them. It was a bit too hot for her liking, between the season and her disguise, but the sun was low enough to cast the area into shadow and was probably the coolest that she could realistically hope for while she recovered from her exertions.
Too tired to worry about the timberwolves being a threat to her at this point, she decided to rest her head and close her eyes, not opposed to accidentally taking a nap since there was still plenty of time before the sun set. A few minutes later, the timberwolf that had a view of her face made a gesture to the others, who acknowledged it with a nod of their heads. All of them proceeded to glow green as they quietly dispersed all of the pieces that their bodies were composed of, which began to float toward her prone form. Detritus from the forest floated into the clearing and joined them as they gathered around her, where they began to form the trunk of a tree.
By the time the darkness that her eyelids, mask and shade provided was darkened even further, enough for her to notice, she was forced into a dreamless slumber before she could investigate the cause.
When Twilight Sparkle failed to leave the forest on time, her friends rushed in to find her despite the hour, doing little to prepare for it aside from bringing some lamps and flashlights. The disturbance they caused not only did a lot to interfere with their search and incur a number of minor injuries, but two of their number wound up needing Fluttershy's help to reverse their petrified status.
When it became apparent that they were going to need help, Fluttershy and Applejack continued the search while the others went back to Ponyville to get more hooves on the case. By dawn they had several proper search parties, and later promised the aid of a scent hound. However, despite their best efforts, all they found of Twilight Sparkle was her pendant, while the dog had favored a sizeable area and hadn't been able to pick out a trail that led to an ultimate destination.
After a week with no success, everyone began to fear the worst. Many had looked about the tree in the clearing, but no one had noticed anything odd about it. Not even Zecora, because she had not been to that area in a long while, due to there being no flora or other things that she needed there, and thus couldn't remember if the tree was a new feature. The princesses, who eventually got involved, didn't have any luck either: Luna couldn't detect whether she was alive or not because she wasn't dreaming, and Celestia couldn't divine her location, something that should have worked even if she had died — in which case, she would have been directed to her remains.
One morning, a soft thump came from within the tree, which repeated more frequently and with more volume as time passed. Eventually, there was a sharp crack and a couple of small fractures appeared through the bark. Before long, bark and wood began to fly off of the tree as a jagged hole was created, which was quickly expanded until its creator could push their upper body through and slump over it in exhaustion.
Twilight Sparkle panted as she squinted her eyes against the sunlight, trying to see what she had been trapped inside of. The last thing that she remembered was lying down to rest after playing with the timberwolves, and it seemed that she had been put inside of a tree somehow. She was even covered all over in tree sap, which was going to be a pain to get out of her coat, mane and tail...
"...Hold on," she thought, as she gave her forelegs a closer look.
Her brow furrowed when she noticed the tree sap slowly sliding down her forelegs, which appeared to be a bit too smooth and reflective to be covered in hair. She touched one with the other, finding little resistance when she rubbed them together, and thought that there might not be any without the tree sap. Then she tapped one foreleg with a hoof, where she heard a clack and felt a sensation that wasn't what she would have expected if she had been wearing something.
Baffled, she turned her head to inspect what she could see of the rest of her body, and discovered more evidence that her timberwolf disguise may not have been replaced by something else: because she appeared to have dragonfly wings, which twitched when her thoughts focused on it. Needing to confirm what she was seeing, and having recovered enough to continue her escape, she pushed against the tree until the rest of her body was dragged out, but not before she tucked her head in so she could roll onto her back.
She lay on her back for a few seconds, after getting a glimpse of her altered underside and hind legs, then she got her hooves underneath her and stood up. Once her legs were straight, she was quick to notice that the ground was farther away than she was accustomed to, revealing that the changes to her body were deeper than she had initially suspected. Said changes, after she got a better view of her body and inspected more of it with her hooves, seemed to be related to some kind of insect. Aside from the wings and exoskeleton, as well as the increased size of her body and horn, though, not much else had changed from when she had been a pony.
Regardless, panic began to well up inside of her, from not knowing what she had become, how she had become it, or how her friends — and ponies in general — would react to her appearance. However, her panic attack was derailed when she realized that she was coming up with answers to some of her questions, answers that she shouldn't have known and hadn't tried to invent. Confused by this, she focused inward and explored the knowledge that she had inherited with her new body.
Apparently, she was a changeling — a queen changeling, to be exact. Changelings fed on various forms of love, and could alter their appearance to inspire them. When a queen could no longer reproduce, they create timberwolves and task them with finding and creating a new queen. The timberwolves have a breath to ward away predators, because they typically didn't have the right mindset to survive as a changeling, and behaved like predators themselves to find someone who was friendly enough to try befriending them instead of fleeing or fighting, which was an attitude that would greatly increase a queen's success.
She mulled over this information until one particular piece of information jumped out at her, which quickly led to her learning how to use it. A flash of purple fire later found her in her original form, even down to the size. Seeing this perked her up immediately, because now she could live her life normally if she wanted to. Then she frowned, since she doubted that she would be able to hide what had happened to her forever, and discovery would probably be problematic. Besides, it would likely be better to reveal what had happened, if for no other reason than to have help transforming herself back to a pony.
In the meantime, though, she had an opportunity to study a species that she'd never heard about before, which was exciting despite being the subject of said study. The shape-shifting ability could prove to yield interesting experiment opportunities as well. She was daunted by the ability to fly, but she — like a lot of earth-bound ponies — wondered what it would be like.
...Speaking of flight, the addition of wings would have made her an alicorn, had they looked like the wings of a pony. She found the idea of becoming a princess to be amusing, especially when she imagined herself ending up being a princess of friendship, between changelings needing sustenance from positive relationships and the fact that she had yet to finish her friendship lessons. She assumed the guise of Celestia, had a giggle about "being" a princess, then resumed being her unicorn self because it might cause a problem if someone saw a changeling before she could explain anything.
And so it was, with an optimistic bounce in her step, that she began her trek back to Ponyville.
Author's Note
(This is the third piece of super garbage that I wrote to amuse myself.)
This is just a product of putting a few flimsy correlations together. Specifically: Chrysalis being birthed from a tree in the comics; said tree being hollow; Chrysalis using trees to create some form of life; timberwolves being made of trees; timberwolves being hollow; timberwolves being interested in fruit, from a tree, that undergoes a transformation; timberwolves maybe having the potential to assume more forms than a bigger wolf; timberwolf magic is green, like a changeling’s.
And then there’s the part where timberwolves look like predators, yet that is undermined by their breath and going through the trouble of acting like it’s choking on a rock... with nonexistent lungs and — what I’m assuming to be — unnecessary air. It’s all very suspicious. 
That aside, this story assumes that the circumstances surrounding Chrysalis’ birth are atypical, with the process and nature being corrupted by the environment as well.