"Wow. I... ah. I never knew your life was so... Difficult" Twilight said, slightly shaken.
"Um, I-I-if y-you don't m-mind me asking, Trixie said timidly, "w-where do I spend the night?"
"Don't worry about it! You can sleep in my bed; I have a spare bed. Spike! Do you know-"
"Got it! I am your number one assistant, remember?" he grinned as he pulled out the spare mattress. Trixie blushed; how long had he been here?
"Thanks Spike." she smiled.
She showed Trixie the way to the washroom and prepared for bed. After cleaning up, the pair made way for bed. Twilight threw on a couple blankets. "Goodnight Spike, goodnight Trixie. We'll make this work out." She said that last part to herself and fell asleep, thinking on what she could to help Trixie.
()()()()()()()()()()()()()()()()()()()()()()()()
The next day, Twilight set out to find her friends. Trixie went along unwillingly.
-earlier-
"w-what if they're still mad?" Trixie whimpered. "T-they have e-every reason to."
"Don't worry about it" if you're going to stay here with me, you’re going to have to apologize.” She added the last part with authority. "Let’s go apologize to Applejack. "
Trixie gulped.
-now-
"Why heya there Twi… Twi, what in tarnation, is she doin' here!?"
"Eep" Trixie suddenly made an excellent Fluttershy impression.
“Calm down Applejack, she’s just here to apologize.” Twilight said.
"Ah don' believe it" AJ announced with contempt. “ ‘Ya dare show yer face ‘round here again-“
"I-....." Trixie apologized incoherently.
"Pardon?" AJ said with a bewildered look on her face. This was the 'great and powerful Trixie they got humiliated by a while back?
"I-I s-said that I w-was s-sorry" Trixie whispered. She looked terrified.
Applejack looked like all her apples grew legs and started tap-dancing. She expected an apology as much as the apples tap-dancing.
"Well, shucks, she did apologize, but how can ah be sure she ain’t lyin'." Applejack shot back. “And wah’ in tarnation is she a filly?” she whispered to Twilight
"Applejack, please, you can trust her, you have no idea what she's been through." Twilight said seriously. “And, when Rainbow Dash did her Sonic Rainboom again, she accidently caused Trixie to use an age-manipulation spell on herself.
"Aww, shoot Twilight, I accept her ‘polagy' but I ain’t trustin’ 'er yet!" she said gruffly.
As she turned to leave, she took a glance at, to see a tear fall from her face. Before she could think of anything else, she started running, wondering if she had been too rough on her.
"Shhh, don’t cry Trixie,” Twilight said gently. She ran her hoof down her mane. “Let’s go find Rarity, and apologize to her next. Don’t worry, I’ll be with you.”
-//--//--//--//--//--//--
"Well I never!" Rarity said when the pair walked into her Boutique. Trixie did her best to hide behind Twilight. “And, err, why are you…small?”
"Calm down Rarity, She's changed. Look at her!" Twilight exclaimed. “and umm, there was an age-manipulation spell problem.”
"Um, hi. " Trixie said nervously. "I-uh..." she went back to hide behind Twilight. Twilight stepped aside.
"Trixie, why did we come here?" Twilight asked sternly.
"I came..."she mumbled out her apology.
"I beg your pardon?" Rarity snapped. Rarity’s angry aura was a bit overwhelming.
"I s-said I-I came t-to say, I'm sorry for ruining your mane... She mumbles silently.
"Well! If you're not going to say anything, then I highly suggest you to leave." Rarity nearly growls.
Trixie panicked. "M-mom...I-I-I m-m-mean T-Twilight, I'm scared." Trixie said with a deep blush on her face.
"I," Twilight faltered. 'Mom?' she wondered. "Rarity, what she's trying to say is that she's really sorry about ruining your mane.”
Rarity was taken aback. Not just with the apology, but with her actions. She seems completely opposite than the last time they met. "I.. err, Apology accepted.”
But Trixie had already run out the Boutique, filled with shame. Yes, Trixie was much younger than Twilight, but she acted like the mother she never had. But Twilight wasn’t her mother... she probably thought that Trixie was mocking her or something. Maybe she could run away again.
"Trixie!" Trixie turned to look back. Twilight was looking for her! She started to run. Trixie did forget one thing though. Lights flashed.
"Silly, I can teleport!" Twilight giggled. But she quickly became somber. "Why did you call me mom?"
"I’m well, actually I am a teenager..."
"And?”
"Even though it’s only been one day, I feel like you actually care about me...like a mom…" Trixie said quietly.
Twilight, despite the situation, giggled. "I'm not that old, you silly filly!" Trixie blushed. Despite the show, Twilight had an idea. This filly was young, and honestly, needed to be re-guided. She couldn't live alone, she needed somebody... She needed a mother. "Do you want me to adopt you as my daughter?" Trixie froze. ‘what? Me? Officially adopted?’ it seemed to good to be true.
"N-no...that’s alright..." Trixie whispered. "Look can I apologize to the rainbow mare later? I-I need to be alone. "
The following week, Trixie hung around the library, helping Spike and Owlowlicious organizing the books and things. She got to know Twilight very well in that time period and was happy. For the first time since Hermes, she was truly happy. Rainbow Dash was on vacation for 2 weeks, so they still had another week until she came back.
"I was serious about adopting you, you know." Twilight said one day.
"I'm still thinking about it." she replied quietly. She was thinking what happened the past week. Pinkie Pie found out about her and wanted to throw a signature party, but Twilight told her to let this pass by quietly. Yesterday she met Fluttershy. It was...incredibly awkward.
She turned to look at Twilight. Unsure of what to say, she just looked down. Then...
"W-what are you doing Twilight?"
"Giving you a hug! You always seemed down, and, you looked like you needed one." Twilight smiled. She thought to herself. Why was she being so…motherly. ‘I know being nice to her is important for her recovery, but, especially after she called me mom, I really feel like I have to take care of her. She’s a teenager again, and somebody needs to re-guide her, maybe make her a better person than she once was. And Pinkie Pie has really rubbed off of me.’ Twilight held on, then patted Trixie on her mane.
Trixie broke out fresh tears, happy tears. She tightened the embrace. She was happy here. Maybe she’ll take Twilight up on her offer.
Ch. 2, first impression:
...this is ominous. I count four problems with Twilight's opening lines alone. Both ellipses need to have spaces after them, "harshly" is an adverb and you're not modifying a verb, and you have no punctuation at the end of the sentence. I haven't seen that anywhere else in this story yet. You should look into getting a proofreader. The pacing also feels a bit fast. I'm going to keep reading though.
Ch. 2, final impression:
Good chapter, small problems. More missing punctuation. Twilight's reaction to Trixie calling her "mom" seemed really flippant. I'm not sure how to address Twilight's idea of adopting Trixie. I mean, my first instinct is to say it seems too... easy, but that's not quite right. Twilight, really, should be willing to do something like that. But it seems like the idea is coming from the wrong place; she's not doing it because Trixie is a child again and really needs somepony to look out for her. And even at that, there hasn't been any mention at all of anypony wanting to try to get Trixie back to her normal age...
Once again, Mr. Papercut has a sharp eye. The pacing is uber quick, I have a problem with this too. I have been able to counter my tendency for blatant and blunt plot developments with description and dialogue. The dialogue in this chapter was much better, by the way. Trixie's 'mom' slip was absolutely adorable, keep that in there.
I like the concept, it's just delivery we have to sort out now. My first suggestion is to take your time. Take it paragraph by paragraph. What helps me is writing out a skeleton first, usually in a different document, where I quickly write out what needs to happen or pivotal pieces of dialogue. Kind of like spark notes, except more in a narrative format. After I do this for the chapter, I start on each piece of skeleton and build a paragraph around it. This serves two mane purposes; The text stays tight and focused and it smooths the flow between ideas and events.
Watch out for those missing words. A couple times I got the feeling that something, a line or two, got left out or was deleted and the surrounding sentences weren't modified to address the change. The point where Trixie is apologizing to Applejack is the biggest example. You got her mannerisms down pretty good, but it felt like there was more that needed to be said. Maybe having her back down just a little, for Twilight's sake. It was a good exercise for setting the tone for the chapter and the other apologies. I would like to see how things went with Fluttershy though.
In a nutshell, it's okay to take your time. Try to work Twilight up to the idea of taking Trixie in. You could probably address the issue of getting her back to her normal age in this very chapter, over the week she stays with Twilight. Perhaps Twilight can't change her back because of the circumstances in which the spell happened. She tries but fails, and deduces that it was the enormous surge in magic caused by the sonic rainboom. Instead of Trixie casting a normal, illusionary spell, she cast a powerful time altering spell. As we learned from It's About Time those spells are hard to do and often you can't duplicate them. Just an idea.
This may seem like a lot criticism, but I will assure you that if I didn't like it, I wouldn't say anything. I really want to see this taken to its full potential. It's a great idea. Imma read more now...
Got a few more problems with this chapter. Why is Twilight giving her her own bed when she has a spare? Seems to me that giving Trixie the spare while she sleeps in her own would be a little less awkward. Also, "Thanks Spike." she smiled, threw on a couple blankets, and fell asleep, thinking on what she could to help Trixie. This was really REALLY rushed. No "Goodnight Spike. Goodnight Trixie", no showing her to her bed, no getting ready for bed, nothing. The way it reads, it sounds like Twilight just fell asleep while Spike and Trixie just stood in front of her. Don't be afraid to describe. Set the environment. This whole chapter reads more like an outline for a story than a full story.
Also, adoption? Trixie has just had her physical age regressed. Her mind is still the same, or she would not recognize Twilight. Trixie has by this time spent several years on her own (by your canon), and is evidently somewhat self-sufficient. This seems like an odd thing to suggest, even for Twilight. Letting her stay with her until she's back on her hooves is one thing, but this is... well, it's just a bit odd. Especially since this is supposedly a Twixie story.
And it would have saved you a lot of rewriting the same event if you had gathered all of Twilight's friends so that she can apologize to them all at once.
Other than that, Laichonious and Little Jackie Papercut pretty much hit the nail on the head.
Jeez. I know she was a jerk last time, aj, rarity, but aren't you two being a bit too harsh here. She's a teenager for celestia's sake!