The first clue was the humming. No matter where they went, Rainbow Dash could be caught lightly humming some determined tune under her breath, occasionally even twitching her neck up and down as if bobbing to some beat only she could hear. Applejack was, of course, the first to call her out on it. She could didn't mind humming on principal – heck, she liked to belt out a few lines of "Don't Wait for Daisy" when she was out bucking by herself in the far Fuji pasture – but three solid weeks of the same song was enough to drive anypony crazy.
"Dash, it sounds like a mighty fine song, but could ya' please reign in the hummin'? Yer drivin' me crazier than Fluttershy's vegetarian ferrets listenin' to a lecture from Derpy Doo." Applejack ground out one afternoon as they gathered around a table for lunch.
"Oooh, Dash's humming a song? I love songs! They go well with parties! And we're having a party! You should sing it aloud so we can all hear it!" Pinkie Pie squealed, completely oblivious to the way Rainbow's coat had suddenly become three shades lighter and the tight, defensive way she was holding her wings.
"Pinkie Pie, this isn't really a party. Just a little luncheon I invited you all to so that we may celebrate Twilight's continued success." Rarity clarified with a little nod of her horn towards a blushing Twilight. "Thirty-five spells is really quite a feat, my dear, and one most certainly worth celebrating."
"All the more reason to have a song for it!" Pinkie Pie announced. It really was a statement about the citizens of Ponyville that no one else in the restaurant even looked up at this.
"I don't know." Rainbow said uneasily. "It doesn't even really go with something like this and I don't wanna take away from Twilight. Applejack's right, I'll just knock it off."
"Awwww!" Pinkie Pie practically melted to the floor in disappointment. "Maybe it's actually the perfect song for today! You never know unless you tell us and we decide! Tell us! Tell us! Tell us!"
"Uhhh…"Rainbow shuffled back a few paces in response to Pinkie's pressing chant. "It's about harmony, I guess. Living together in harmony forever." If at all possible, she clenched her wings even tighter.
"Really?" An enormous grin spread over Pinkie Pie's face. "I know that song! It's perfect!" She bellowed. "I don't why I didn't think of it before!"
"Uh, Pinkie—" Twilight tried to cut her off but it was too late. She was off, a magnificent pink blur belting out:
In harmony
Harmony
You're you, I'm me
Together we
Can live in harmony
In the resulting confusion (If there was only one note/How boring life would be!) no one noticed how Rainbow quietly let a sigh of relief escape her mouth.
The next clue was a little more obvious. Cheerilee had just started the very large and complicated unit on magic in Equestria, explaining how very important magic was in everypony's life. And to make things even more special, the teacher for Scootaloo and Sweetie Bell's class had come down with a cold, forcing Cheerilee to combine the two classes today. It was no wonder the lesson took a turn for the crazy.
"Okay class, settle down please." Eighteen young ponies, crammed into a room meant for nine, stilled in their fidgeting and talking, at least for next ten minutes. Cheerilee breathed a sigh of thanks and smiled at them all. "Thank you. Now today we are going to continue our discussion on how everypony in Equestria uses magic. Did you all ask your friends and family how they use magic? Yes Sweetie Bell?"
"Rarity uses her magic to move all the things needed to make one of her dresses." She said.
"That's right, as a unicorn, Rarity uses magic in a very visible way. How about other types of ponies? Yes Applebloom?"
"Applejack says Earth Pony magic is what gives her and Big Macintosh their strength to do all that applebuckin'." She announced proudly, nudging her nose slightly higher in defiance once the whispers and snickers about poor farmer ponies reached her ears.
"You are absolutely correct, Applebloom." Cheerilee said. She narrowed in on the two snickering fillies on either side of poor Applebloom and summoned up her best teacher voice. "Diamond Tiara, Silver Spoon, do either of you have something you'd like to add?"
Unsurprisingly, it was Diamond Tiara who responded.
"My mother told me that a pony's coat color was magic. Otherwise everypony's coat would be just like parents' and somepony's herd would be stuck with all the yucky colors. And it's why my coat is so perfectly magenta, unlike any one else in my herd." It was at that moment Cheerilee started to silently panic while her class broke out in noisy confusion.
"What?"
"Really? Is that why my mommy's coat is pink and I'm green?"
"Naw, that's impossible. My dad's coat is blue and that's why I'm blue."
"Cheerilee, is that true?" Several plaintive voices rang out at once as everyone began twisting around in their seat to suddenly examine their coat and compare it against the other coats and manes found in town.
"Now if everypony can please calm down." Cheerilee cooed sweetly. She cooed with a little extra sweetness at Diamond Tiara."Now it is true that a pony's colors are not necessarily going to be the same as his or her parents' colors, especially when it comes to colors of his or her mane. But nopony knows for sure what causes each pony to be born with certain colors, but I have heard that the leading theory is a combination of magic and genetics. So Diamond Tiara is partially correct." Cheerilee finished with a quick look at each of her young pupils. They appeared to be stunned into a welcomed silence. Then Archer slowly raised a hoof.
"Yes Archer?"
"What are genetics?"
"Oh, I know!" Twist squeaked excitedly as Cheerilee's heart plummeted even further than before. "It's the stuff everypony has inside them makes up everything about them! Then you mix your stuff together with another pony's stuff so the filly or colt gets a little bit of both parents."
"You mean like blood?" Diamond Tiara demanded in a horrified voice as Cheerilee struggled not to faint at Twist's fantastic description of "mixing stuff together." "I thought it was just reason why everypony in my herd has perfectly violet colored hair. Not something completely gross like blood."
"Blood's not gross, it's natural!" shouted Tornado Bolt, who was seated on the farthest away from Diamond's glare and felt safe enough to defend science. The entire class seemed to swell and was poised on bursting out into another loud argument when Coronet's question rose above the general hubbub.
"What do you mean, somepony's herd would be stuck with the yucky colors? What colors are yucky?" Diamond Tiara actually seemed to blush at this.
"Well, you know, stuff like yellow and brown and gray. Boring colors."
"Hey, my coat is yellow. That's not nice!" Sunny Daze protested.
"Doctor Whooves has a brown coat and a brown mane. There's no way he's boring." Archer said.
"Silver Spoon is gray." Twist pointed out. "Maybe you need your eyes checked out. My doctor's really good, I can get you an appointment with her if you want."
All Cheerilee could think as she rallied the class back to order and attention, was thank Celestia that this time no pony had thought to ask how genetics are mixed.