Scootaloo heard the window unlatch from downstairs. She didn't even bother to go up and look; what happened was obvious.
"Dang it," she swore before wiping at her eyes again. The truth began to sink in like poison; Fluttershy left, and they were all alone.
"Scoo!" Storm seemed to notice her sister's troubles as she began crawling towards the weeping filly.
Scootaloo looked down at the filly before taking her in her arms. "It should've been Fluttershy." she mumbled darkly. "Why Rainbow? It should've been Fluttershy."

"You going flying Rainbow?" a much more energetic orange filly stood in front of the mare in question.
"Yeah, I'll be back soon squirt," she patted the filly's head affectionately, or Rainbow's definition of affectionate.
"Be careful dear," Fluttershy walked in, carrying little Storm who was chomping on her mane. "Cloudsdale's trying to get a storm under control and they've lost a few stray clouds."
"Ehh, I'll be fine. Have you forgot who you're married to?" She kissed the yellow pegasus on the lips, causing Scootaloo to grimace.
"Eww."
Rainbow laughed. "Don't worry Scoots. I used to think kissing was gross too." she looked back at Fluttershy, affection evident in her eyes. "Trust me, it's not that bad."
"It is too. What makes it even more gross is when you stare at each other all lovey dovey."
The filly's comment gained a laugh from both mares.
"You'll think different when you grow up and find the right stallion." Rainbow glanced back at her wife again. "Or mare."
"You're doing it again!"
"Ok squirt," she ruffled Scootaloo's mane. "Well, gotta dash. Be back soon, I promise!"
And with that, Rainbow took off, leaving the house for the last time.

Scootaloo continued to stare out the window, listening to the rain batting at the exterior of the home. It started raining like this later that same evening after Rainbow left. When some employees from the Cloudsdale Weather Corp showed up, announcing the tragic news. A stray cloud had reached Ponyville, knocking Rainbow off her flying course. Before she could regain control, she smacked her head against a tree. She died before they could get her to the hospital.
Fluttershy thanked the employees before retreating to her room. She didn't come out for three days.
Scootaloo let a few more tears fall, before reluctantly deciding upon closing the window upstairs. She didn't want the room to get wet, but by now would it really matter? Fluttershy left, so obviously there would be nopony staying in there. But still, if too much rainwater got in there it would soak the cloud floors possibly causing a roof leak downstairs.
Stiffly getting up, the orange filly left her sister and trudged upstairs.
The room had indeed been soaked quite a bit. Half of the bedspread was dripping and parts of the floor felt spongy when the filly's hooves made contact with them.
Wind whistled through the open window, enveloping Scootaloo as she reached it. She shivered as she swung it shut.
"Stupid," she muttered as she reached for the latch. But her hoof stopped in midair as she caught sight of a tiny yellow spot on the ground below. "What?"
Rubbing away the fog from her breath, she leaned over to get a closer look. Still a yellow spot. Nothing distinguishable about it.
What if?
Scootaloo shook her head. It couldn't be. Fluttershy was long gone; probably off in the Everfree Forest to hang herself.
But it's still possible
"Shut up!" she screamed. "It's not her! It's probably some stupid animal!"
She turned away, but a nagging feeling still tugged in her chest.
"Grr!"
Turning back around she made a brisk move for the window, pushing it back open again.

The decent downward wasn't an easy one. Scootaloo only had mild experience with gliding and almost none when it came to heavy diving. Her front hooves were held out in front of her, eyes squinted as wet strands of mane clung to her forehead. The yellow spot slowly became more distinguishable, speckles of pink slowly becoming visible.
"C'mon!"
The ground was approaching fast as the orange filly struggled to open her wings.
"C'mon!"
Her damp wings clung to their upward position.
"C'mon!"
Clenching her teeth, she channeled every ounce of energy into her wings. And slowly she began to bring them out.
The wind snagged at them constantly, pushing on them like tiny parachutes. No, she wouldn't have it; She struggled to push them back out, but the wind eventually outnumbered her by force eventually snapping them upward again.
The ground was less than twenty feet away.
"FLUTTERSHY HELP ME!"
The uncontrollable cry was surprisingly answered as Scootaloo felt herself landing roughly into somepony's hooves several seconds later. Opening her eyes, she was met with a familiar yellow embrace as they both descended safely to the ground.
A second after touchdown, Scootaloo seized the opportunity to jump down.
"WHAT THE HELL WERE YOU THINKING, LEAVING US LIKE THAT?!"
Fluttershy stared back at the orange filly, her expression unreadable. It was then that Scootaloo noticed her condition. A cut ran across one of her eyelids, her mane was a ruffled mess, and parts of her legs and tail were covered in mud.
"I was looking for Rainbow," her voice held as much expression as her face.
"SHE'S DEAD YOU IDIOT! SHE'S DEAD AND THERE'S NOT A FREAKING THING YOU CAN DO ABOUT IT!" tears began to leak from the filly's eyes. "She's not coming back no matter how much you want her to."
This comment seemed to snap Fluttershy out of her trance. "What?"
"You heard me," Scootaloo turned away. "I had to grasp reality when my parents left me on the orphanage doorstep. 'Oh we'll be back Scootaloo. Wait there for Mommy and Daddy. That's a good girl.'"
The mention seemed to resurface old memories as the filly began to sob softly.
"Scootaloo," The mare tried to approach her, but got a cold shoulder in return.
"No, the way you act makes you no better than them." She turned to face Fluttershy again. "Goodbye Fluttershy."
"Scoot-"
"No!" Scootaloo turned around again, beginning to walk away.
"Scoot, I'm sorry!"
"Heard that before."
"Scootaloo," The yellow pegasus sighed, a few tears straying from her eyes. "Baby, please...don't do this."
"Why?" the filly turned her head. "Don't want something else to feel bad about? Well you've let me down too many times. If there's anypony to blame it's yourself."
"Scoot." Fluttershy reached out a hoof desperately. "I love you."
This seemed to soften the filly's resolve, but only for a second. Her next answer was curt. "Call me back when you've coped enough to take care of yourself again. Don't do to Storm like you did to me."
With that Scootaloo continued walking, Fluttershy's desperate calls falling on deaf ears, eventually fading with the rain and the wind that continued over the mountains beyond.

Author's Note

So yeah, end of two parter. I'm such a hypocrite. Hate sad endings but I make one myself XD Constructive Criticism is welcome ^^ And a big thanks to everyone that commented on the first part :D And the followers I've gained, You guys are the best!