Well, that took longer than I expected, but such is the way of things when you're the sort of person who would rather be satisfied with what you've created, and the first few versions are not satisfactory for whatever reason.
Also, I bumped this up to teen to be on the safe side. There's a bit of content in the first paragraph that may warrant that.
And on that note, enjoy. :)
Fortunately for Rainbow, she's the sort of pony that can fall asleep anytime, anywhere, so long as it's not too noisy. Unfortunately, her subconscious decided to use this opportunity to make her feelings undeniable, even if it did embarrass her. Throughout the night, she dreamed about flying with Fluttershy, cuddling with her, and a few dreams involving more... intimate activities.
Now, none of this would be a problem if her subconscious had any sense of timing, but it doesn't, or maybe it does, and decided to have some fun with her, because when it was time to wake up, it was right in the middle of one of these more intimate dreams, and she decided to wait a minute or four to enjoy it before waking up. Well, until she felt hooves shaking her and heard a soft but compelling voice telling her to wake up.
Opening her eyes and seeing Fluttershy after having a dream like that was not how Rainbow Dash wanted to start the day. Her heart started to race and she fought to keep her facial expression under control, hoping she didn't say anything embarrassing or racy in her sleep. Judging by the expression on Fluttershy's face, she didn't have to worry about that, however, and, with the dream she had still on her mind, she got up on all fours and walked over to the camp fire, ready for breakfast.
Over breakfast, a curious Fluttershy asked Luna, “What does the princess of the night do? Other than raising and lowering the moon, I mean.”
“Well, I hold night court, hearing out the few petitioners who would rather deal with me instead of my sister, for various reasons. It's quite dull, usually, but it does allow me to catch up on the times. I have a few other duties that I choose not to disclose as well,” Luna said, making another valiant attempt to stop using the Royal We.
“Why would petitioners come at night?” Rainbow asked.
“If I had to guess their reason, I would say that, maybe a third come during the night because it's the only time their schedule allows, a quarter because they have fallen out of favor with my sister and wrongly think I'll be willing to deal with them, and another quarter because they think I am going to be easier to manipulate than her. I really love crushing that last group's expectations under my heel. The rest have their reasons, that I choose not to speculate on,” Luna said.
“But isn't that mean, crushing their expectations like that?”
“It is, but that's the risk you take when you deal with royalty, especially when you try to manipulate royalty to your own ends, instead of trying to work with us.”
“Oh,” Fluttershy said, slightly worried.
“Do not worry. My sister and I have no intention of doing anything like that with you or the other bearers of the Elements of Harmony. We have only respect for you, as you have saved Equestria twice now, even if you had to save it from me once.”
Fluttershy blushed and gave a small smile at hearing this, but said nothing. Not long after, they packed up and headed out
Landing at their next spot, four hours later, they could see the edge of the forest. Rainbow decided to take care of a small but important matter while Luna prepared their tea. All three of them knew they would be sick of green tea by the end of this, but it was far better than dealing with the trots for a couple of days at best or violent illness at worst.
Her bladder dealt with, Rainbow managed to get Fluttershy out of Luna's sight and earshot without alerting her, as she really didn't want to risk a generally reasonable but very out of date ruler stumbling on two mares possibly getting romantically involved. After making sure that Luna wouldn't bother them, she said to her longtime friend, “Fluttershy, I have something to tell you.”
“Yes?” Fluttershy asked, her voice revealing nothing.
“I uh...I...Oh, buck it,” the impulsive blue Pegasus said, before wrapping her forelegs around Fluttershy's neck and giving her a big kiss.
Now, if you had asked Rainbow Dash how she would expect Fluttershy to react to being kissed like that, she probably would tell you that she would think that Fluttershy would kiss back, or at least accept it. Unfortunately for Dash, neither of those things happened. Instead, she found that Fluttershy was trying to pull away, her hooves scrabbling on the ground, looking for traction. Rainbow released her, and found herself looking at a very shocked Pegasus.
Before Rainbow could think straight enough to to consider how she should respond to what had happened, Fluttershy said, “I don't know what to say.”
“Can you just answer one question for me?” Rainbow asked, getting things together enough to seek an answer to the question eating at her.
“Okay,” a confused Fluttershy said.
“Do you love me?”
It took her a few seconds to respond, but she when she did, the answer was not what Rainbow had expected at all. “I'm sorry, but I don't know. I really don't.”
It was Rainbow's turn to be shocked. She had never thought that Fluttershy, of all ponies, wouldn't be sure of her feelings, and her answer was worse in some ways than a simple rejection. If she had just said no, Rainbow might have been hurt, but at least she would know where she stood, but this didn't even allow that. She asked, with surprise lacing her voice, “How can you not know?”
“I guess I never really thought about it, but if you give me some time, I can give you an answer.”
Rainbow, confused and unsure what to do, started saying something, but cut herself off, not wanting to risk hurting Fluttershy. After taking a moment to calm down and get her thoughts in order, she started again, saying, “Listen, take all the time you need to figure things out. I'll wait.” Rainbow may be fast thinking and impulsive, but even she realized that she would have to be patient if she wanted to have any chance with Fluttershy.
Fluttershy nodded, and walked back towards their camp, ready for lunch. Rainbow, hoping that Fluttershy would reciprocate at some point, followed close behind.
Luna could tell that there was something up between the two mares, but couldn't place it. As she handed them their tea, she watched them, noting how Rainbow kept glancing at Fluttershy when she thought the latter wasn't looking, and how Fluttershy looked conflicted about something. She debated speaking up for a few minutes, before deciding that it would be better to try to find out what was going on. “So, when you two disappeared over that hill, something obviously happened. May I ask what?”
“I don't want to talk about it,” Rainbow Dash said.
“Fluttershy?”
Fluttershy shrank back, shaking her head.
“Okay, it seems we will not be getting answers for now,” Luna said, slipping back into using the royal we, “but we will say that if either of you two has a problem, we would be happy to help.”
Both Pegasi gave a quick thanks, then sat in silence while they ate, tempests raging in their minds.
Rainbow Dash was struggling to figure out whether she should try to hurry along Fluttershy's decision, and how she should go about that. Numerous ideas, and their potential pitfalls whizzed through her mind. About the only decision she came to at this point was that just being helpful and understanding of the timid Pegasus would help things along.
Fluttershy, on the other hand, had a more complicated and intractable problem. She had to figure out all the myriad feelings she had towards Rainbow Dash. Some were positive, others negative. Some were intense, others barely noticeable. The one thing they all had in common, though, is that they were hard to identify, though mostly because there were a lot of them. She was glad that Rainbow wasn't pressuring her to make a quick decision, but she had to wonder if she would move onto someone else if she took too long. She quickly put that thought out of her mind however, deciding that it would be best to just get her feelings in order, and not worry about whether this or that would happen.
After lunch, both ponies did get up and move but neither went far, being too enamored in their thoughts to navigate somewhere too distant. This would prove fateful.
Two hours after lunch, everypony was still resting, save Rainbow, who decided a nap was in order, when a rustling of leaves drew their attention. The two wakeful ponies turned towards the source of the sound, confused, since they had not encountered very much wildlife during this trip.
Confusion, however, turned to fear when a chicken's head with red eyes popped out of the bush. A quick yelp from Luna woke Rainbow up, and the rainbow maned pony was about to complain when she saw the cockatrice. Abandoning all reason, as a pony like Rainbow Dash has a tendency to do, she rushed off to take it face to face right up until it looked her in the eye.
Fortunately for Rainbow, the cockatrice was blown off its feet before she could be turned completely to stone, thanks to a quick bolt from Luna's horn. Unfortunately, she was now halfway turned to stone, and the cockatrice was still very much alive as Luna hadn't fired a very powerful bolt.
The cockatrice quickly recovered from the blow it took, and turned to stare down the one who had shot it, when Fluttershy put herself between it and its target, and began to use The Stare and issue a verbal beat-down not unlike the one she gave to the cockatrice that had attacked Twilight and the Cutie Mark Crusaders. She felt her body transforming into stone, but ignored it. Her friends were in danger, and she was not going to back down. She would save them or die trying.
Seeing this angry pony using something that served to deliver immense fear to its heart, the cockatrice redoubled its efforts, but it wasn't enough. Eventually, terrified, and unable to resist the strange magicks of the pegasus in front of it, the cockatrice transformed both of its victims back to normal, and ran off.
Luna watched this whole scene, jaw agape. Se was amazed to see The Stare slow the transformation of the Pegasus into a statue to a crawl, and drive off the cockatrice, a creature known to be persistent in their efforts. She watched with equal amazement as the cockatrice reversed the effects of its magic on both Pegasi, freeing them from their stony prisons.
Rainbow Dash, now able to move about again, told Fluttershy, “You saved me.”
“No, Luna saved you. I just drove the cockatrice off. But I'm glad to see you're okay,” Fluttershy said, giving her friend a warm hug. The cockatrice had probably only stuck around for thirty seconds tops, after coming out of that bush, but, to the three of them, it felt like it had been hours.
“Thank you both,” Rainbow said, returning the hug and trying to shake off the lingering fear.
“We are happy to help,” Luna said, “But now we are more curious about the stare. We did not expect it to actually slow the cockatrice's transforming you into stone.”
“It did the same thing when I was protecting three fillies from another cockatrice, and when I encountered my first cockatrice. I don't know why but it seems to protect me from their magical effects.”
“Are you sure you cannot control it?”
“Yes. It refused to come out until I saw what had happened to Rainbow,” Fluttershy said.
“Well, we guess this strange power is to thank for all three of us not being turned to stone. Thank you again, Fluttershy.”
“Happy to help,” Fluttershy said, before walking off, obviously still dealing with the events that had transpired. Rainbow, still a bit traumatized by being turned partly to stone for a minute or so also walked off, leaving Luna alone to contemplate what had happened by herself.
A few hours later, they were heading off again, this time landing at the edge of the forest. For the most part, everypony had gotten over the incident with the cockatrice, but they were still on edge, setting up camp well away from any shrubbery, and carefully scanning the area for anything that might be dangerous. When they were sure that they were safe, they set up camp, which was much easier than the first day's attempts due to having some practice. Noting this, Luna rescinded the mental note to send the pole maker to the royal dungeons for a day.
Over dinner, there was noticeably less tension between the three ponies which wasn't surprising considering that they had fought off a cockatrice together. Luna, not wanting to think about that incident, asked Rainbow, “Why do you think you are qualified to be a wonderbolt?”
“Well, I am the fastest and most talented flier in Equestria.”
“Yet you are an individual stunt flier. They are a tandem group. Do you think you could adapt to the change in style?”
“I think I could.”
“But are you sure? If you made a mistake, you or one of the other Wonderbolts could be badly hurt or killed. Do you think you can make transition of style smoothly enough to keep that from happening?”
“Yeah, I think I can,” Rainbow said, getting annoyed.
“We will hope you're right, if you do manage to join the Wonderbolts. We would rather not deal with losing any of Equestria's best fliers due to a flight error if we can avoid it. Also, Fluttershy, we are curious, how did you discover The Stare?”
“Um...It's a long story. I'll tell you when we get back to Ponyville.”
“As you wish.”
Dinner ended shortly thereafter, and Fluttershy went to the edge of the river and lay down, sure that nothing would attack from this direction, and feeling like just appreciating nature and peace for a while.
Rainbow, also having had more than enough excitement for one day, joined her a few minutes later, trying not to let her presence be known. She lay down next to the yellow Pegasus, and looked out on the horizon, content to be with the mare she loved.
Apparently, though, her attempts at going unnoticed had failed, because Fluttershy asked, “what do you see in me?”
“What do you mean?” Rainbow asked, honestly confused.
“Why would a pony like you love someone like me? I'm weak, timid, fearful-”
“Listen, Fluttershy, you're too hard on yourself.”
“I am?” Fluttershy asked.
“Yeah. Sure you're not a strong flier, and you are timid, but you're also one of the kindest, gentlest, most beautiful, and most terrifying ponies in Equestria.”
“Terrifying? Really?”
“Yeah. When you use that stare, I don't think there's anyone or anything that can even pretend that they can stand up to you. And, either way, you're a lot braver than you think,” Rainbow pointed out.
“No, I'm not.”
“Yes you are. Who was it that walked right up to a raging manticore, made a dragon cry, and stared down that cockatrice?”
Well, I guess...”
“Listen, I know you're timid and jumpy, but I've seen how truly courageous you are when your friends are in danger, and that's why I know that when things are going sideways, you're the one pony I want at my side.”
“Really?” Fluttershy asked, a bit of elation in her voice.
“Really.”