Spike didn't really spend that much time with Scootaloo, it had to be said. Heck, he didn't really spend that much time with any of the other kids in Ponyville, and as such he couldn't really claim to know them anywhere close to how well they all knew each other. And yet, as he looked to that little filly, something in his gut told him that something was up with her. She didn't show it, at least not overtly, yet all the little and subtle motions and facial movements as she walked away from him seemed to suggest a problem. Now Spike would, at least at first, think that maybe he should just leave well alone. After all, personal problems weren't always going to be something you wanted others getting involved with. Yet, for whatever reason, he just felt like this specific case needed his input. So, after flapping his wings, he hovered on over to Scootaloo. And the sounds of those wings easily alerted the filly to his presence, and she spun in place, putting on an obviously-forced smile for his benefit.
"Oh, hey there, Spike! How're you doing?"
Landing beside her, Spike raised an eyebrow and folded his arms.
"You know, I was about to ask you that question."
Instantly realising why Spike was here, Scootaloo looked away, trying to hide her face, which was already twisting into one of discomfort.
"Oh! Yeah! I'm totally fine! Why...why'd you ask?"
Now Spike knew for certain that something was up with her, and he walked a few steps around to see her face. Sure enough, Scootaloo turned even more, much to Spike's worry.
"It's just...you seemed a bit off after I came back into town today."
But Scootaloo waved him off.
"Pfft! What? Me? Nah! I'm totally stoked for you, Spike! I mean, wow, wings eh? That's totally awesome and stuff, right?"
Now, it had to be said that Spike was indeed happy about his new flying ability. After all, when you spend your whole life as someone who feels that they don't measure up to others of their own kind, finally managing to achieve something they can do is a serious boost to your sense of self-worth. And while Spike's initial feelings upon learning of this change were ones of fear of rejection from Twilight, he'd learned to feel happy that this had happened to him. But happiness is definitely not what the young drake was feeling from Scootaloo right now, and he was sure to let her know it.
"Scootaloo...I've seen enough ponies in this town try to hide when they're upset about something, and right now, I'm seeing that in you."
Scootaloo couldn't deny that he had a point. After all, having ponies be unhappy and try to hide it was not exactly a rare occurrence around here. And while she initially felt some shame at having been spotted this way so easily, she eventually relented, sighing heavily and letting her shoulders slump.
"Spike, I...I am happy for you. Really, I am. Being able to fly, it must feel great."
Spike raised an eyebrow.
"But...?"
Scootaloo grimaced here.
"But...I'm sorry, I can't help it. It just reminds me of...well...this."
To demonstrate her point, Scootaloo stretched out one of her small wings, looking to them with clear disdain. Immediately, Spike understood, and his inquisitive look was instead replaced with one of understanding, as well as some discomfort of his own.
"Oh...I see."
Silence fell between the two youths, as neither wanted to be the first to speak during such a difficult moment. But at last, after a full two minutes Spike finally did so, looking to Scootaloo and gently placing a claw upon her shoulder.
"Hey, I'm...I'm sorry."
Scootaloo shook her head.
"No, I'm sorry. This isn't your fault. Not your wings, and not mine."
She walked away, but only for a few steps.
"It's just, whenever we were around each other, there would always be something I'd feel about you. You were a dragon, but you couldn't fly."
Pausing, she looked back to him.
"And I'm a pegasus, but I couldn't fly either."
She gestured to herself, then to him.
"Both of us come from people who are known for being able to fly, yet here we were, both kids from those two groups who couldn't."
Again, Scootaloo looked ashamed, staring down at the ground.
"I guess it's just something I figured we had in common."
Spike didn't know what to say. How long had Scootaloo felt this way? Was that really something the two had in common? Had he himself felt that way at some point? He didn't know any answers to these questions, but what he did know was that a friend of his was unhappy, and he was going to make sure to do all he could to fix that. So, taking a step closer, the dragon soon got her attention, and she looked to him with tear-filled eyes, though her despair hadn't yet reached the point where they were falling down her cheek. Spike, in spite of the mood of the moment, smiled.
"Hey, we're still friends, Scootaloo. I know I've changed recently, but that doesn't mean you and I have to grow apart from one another."
He shrugged.
"And I know I'm not anywhere near as close to you as Sweetie Belle or Apple Bloom, but I still valued having you in my life."
His smiled widened a bit.
"But you know what else? You being unable to fly wasn't something I ever even considered when we've known each other."
Scootaloo looked to him, slightly confused.
"But...how could you not think about that? It's something everycreature knows about me!"
Spike nodded.
"Yeah, I know. But did Sweetie Belle become friends with you because you couldn't fly? Did Apple Bloom?"
A blush crept onto Scootaloo's cheeks, and she shook her head, giving him his answer. Spike nodded.
"No. They became friends with you because you're a good and wonderful pony, Scootaloo. Yeah, you and I had 'no flying' as something similar, but similarities aren't a foundation for friendship."
He turned, looking out at the School of Friendship.
"If there's one thing I've learned in all the time I've been with Twilight, it's that people, big and small, feathered or scaly, airborne or grounded, can and should be friends. You don't need to have things in common to be close to one another. Gallus and Ocellus don't, Yona and Smolder don't..."
He turned back to her, reaching out and holding her by the hoof.
"...and you and I don't either."
To say that Scootaloo was feeling touched by Spike's words would have been an understatement, as her tears of sorrow now became tears of joy, and she leapt forward, embracing him in a surprise hug. Though definitely taken aback by this unexpected cuddle, Spike eventually smiled back, reciprocating the embrace. For a time, they stayed together, but they eventually parted, with Scootaloo wiping the tears from her eyes.
"I'm...I'm sorry for feeling down like that."
But Spike shook his head.
"Hey, nocreature should ever be sorry for feeling sad. You had good reason. And I'm just happy I was able to help you."
Scootaloo chortled a little, but her smile faded briefly as she looked again to her own wings.
"I guess this does still mean I'm the only one here who's supposed to fly but can't."
Spike still smiled to her, and when she finally looked back to him, he showed why.
"Maybe not. But you don't need to fly to do great things, Scoots. Twilight did a whole bunch of stuff before ever getting her wings, and so did I."
He pointed to her confidently.
"And I'm sure you'll do lots of awesome stuff without ever needing to fly too!"
Again, Scootaloo was pleased by the words, and she reached out and patted Spike on the shoulder in a manner not dissimilar to what he'd done to her earlier.
"Thanks, Spike. Guess all I needed was to talk to a friend."
Spike chuckled, scratching the back of his head with a slight blush.
"Hehe, no problem. Although..."
He looked to his back, and to his own wings, before glancing back to the filly.
"...if you like...would you like me to maybe take you around...up there?"
He pointed upwards, to the sky, and so did Scootaloo. After thinking on that, the filly looked back to him, her face now bearing a wide and happy grin.
"I thought you'd never ask."
Author's Note
For some years now, this is a headcanon that myself and some of my friends have batted around as a possible cause for Scootaloo and Spike connecting on some level. But, with Spike changing the way that he did, I figured that, if such a connection did exist between the two kids, something like this might probably throw a wrench into it. So I thought maybe I'd write to explore that 
