Prologue - Aftermath of the Storm
It was a stormy day that day... on the shores of Basalt Beach, a terrible incident had happened. Upon a failure to negotiate with the local hippogriffs, six ponies and one dragon emerged from the seas surrounding Mount Aris and managed to make it back to shore. They climbed onto the sand, panting hard as they tried to come to grips with what just happened.
Applejack was the first to speak up. "What were you thinkin', Twilight? I mean, stealin' their pearl?"
Twilight Sparkle tried to steel herself to speak up and could only bring herself to try and justify her actions. "It was the only way to save Equestria..."
"Except it wasn't." Pinkie Pie spoke up. "The queen was going to say yes! We did what you told us and that's what made her realize we were ponies worth saving." She gasped as she came to a startling realization, then turned sour. "Unless... you didn't really want us to show her the best time ever! You just wanted us to distract her!"
The others who were present gasped as they felt a sharp pain in their souls. Twilight continued to speak. "I wouldn't have done it, but this isn't Equestria! We can't just dance around with con artists, make Rainbooms in the sky and expect everything to work out! It's not enough! We are not enough!"
Pinkie, now seething with a tranquil fury, responded. "No, Twilight. We stuck together! We were gonna get the help we needed! The only thing that stopped us... was you!"
"Well, I'm doing the best I can!" Twilight continued. "It's all on me. I'm the one Tempest wants. I'm the last princess!"
"You're also the only one who doesn't trust her friends!"
Finally reaching her breaking point, Twilight uttered the worst words she'd ever spoken to anyone as her horn glowed as if to strike the pink pony.
"Well maybe I would have been better off without friends like you!"
Upon hearing this, Pinkie's soul was absolutely crushed. Twilight realized too little, too late what she had said... the other ponies, feeling hurt, began to trot away from their friend of so long in despair. Some felt legitimately damaged by it... others were just disappointed in her.
Twilight looked to Pinkie in remorse. "Pinkie, I..."
All Pinkie could do was muster a soft, sorrowful "I just can't talk to you right now."
Distraught, they all briefly went their separate ways. Spike, Twilight's longtime dragon companion, went to check on his legal guardian.
"Twilight?" He softly spoke. "It's okay. You'll figure it out."
Twilight could only speak through tearful whimpering as she spoke. "No. I can't... I ruined everything. There's no chance to save Equestria now. It's all my fault..." A bout of silence overcame the area all of a sudden. "Spike...?" As she looked behind her, she gasped in horror as one of Tempest Shadow's minions held Spike hostage.
Spike tried to warn Twilight, but he couldn't stop what happened next: a cage dropped on Twilight, ensnaring her in an unbreakable prison. "No, no, no no no! NOOOO!"
As the cage lifted her up into Tempest Shadow's airship, all Twilight could do was cry out Spike's name as he managed to escape. The final Princess of Equestria had been captured...
Twilight woke up, screaming in a cold sweat. She was back in her bed at the castle, tears streaming down her face as she looked around, letting the sight of her room briefly calm her down.
Spike walked into the room, worried about his friend. "Twilight? I heard you screaming again... you were having the same nightmare, weren't you?" Twilight solemnly nodded. "You've been having that for three weeks straight, now; I think you need some therapy before you end up making your own Tantabus."
Twilight just sighed and looked down, unable to even look at Spike. "Frankly, I'd rather have a Tantabus torture me than have to go through all that again... I just don't understand why I did what I did. You know me better than that! I mean, I've made some pretty big mistakes before, but attempting to steal the Pearl of Transformation? I don't even know what I was thinking!"
"Twilight..."
The purple pony continued. "I can't even fathom why I would think 'oh yeah, stealing their prized artifact is a wonderful idea! I'm sure nothing will go wrong!'"
Spike tried to remind her of her own reasoning at the time. "To be fair, friendship didn't appear to be working... You only did what you thought was good for Equestria. And besides, you did gain a lot of allies in the long run. Heck, we at least got Princess Skystar's help, and Queen Novo's already forgiven you. Right?"
Twilight only looked away. "We did save everypony... But it still bothers me that all this happened. Besides, now that I think about it, everypony was acting less like themselves than usual."
Spike seemed confused. "What do you mean? They seemed perfectly fine to me."
"You're right; they seemed that way. Just like I seemed to have everything under control. They seemed less dynamic than they usually were; like all those lessons over the years were lost on them. Like they were lost on us." Twilight started thinking hard about it like she usually did. "There has to be a logical explanation. There has to be something causing us to lose sight of who we truly are."
Spike looked at Twilight, more worried than ever. "Look, it's like I said before: you'll figure it out. But right now, you need some sleep. How about I join you tonight?"
Twilight smiled at that offer. "Thank you, Spike... I'd love that."
Spike crawled into bed with Twilight and cuddled with her. "I'm betting the other ponies are feeling the same way you do about themselves. I mean, that whole experience affected all of them to an extent."
Twilight sighed. "I just don't know... We'll have to try and find out for ourselves tomorrow."
Spike nodded in agreement. "Well, look on the bright side: at least it couldn't possibly get any worse, right? Compromising your morals and dismissing your friends is as bad as it gets."
Twilight just held Spike close in response.
"Ack! W-Was it something I said?"
"Spike? I want you to promise something..." Twilight spoke more seriously than ever before. "Don't ever let me do something like that again. I'm asking you as my assistant and as my friend. I don't want to lose you, or the other ponies, ever again."
An embarrassed Spike looked up to Twilight's face. "R-Right... I promise I'll try to rein you in... just please stop smothering me with your chest fur..."
Twilight meeped and loosened her grip. "I'm so sorry, Spike!"
Spike: "Hey, no biggie... let's just get some sleep."
The two of them began to drift off to sleep, Twilight finally finding some comfort in her dragon friend... only for her to suddenly shout out.
"Oh my gosh, I just realized I could have turned into a mouse and crawled out of Tempest Shadow's cage! What in Tartarus' name was wrong with me that day?"
Spike sighed and rolled his eyes before going back to comforting her, still smiling. "This might be a long night."
Meanwhile, another world resided in a different plane of existence. High above the clouds was a series of floating islands with different structures and statues dedicated to a divine being. Within the biggest one, a brown-haired boy with a white chiton robe resided, hurrying along as if he was late for something. Eventually, he appeared before several short, winged warriors with golden armor and bows, all preparing to serve their leader.
The boy spoke eagerly and tiredly. "Sorry to keep you all waiting! The divine alarm clock ended up running outta batteries today, so I really had to hurry. I hope I'm not too late for anything!"
One of the small warriors responded. "We are willing to serve you no matter what, Captain!"
"Er... not exactly answering my questions, guys..."
"Don't worry about them, Pit; you know how the Centurions are." A beautiful young woman with green hair, a white-and-gold dress and a matching laurel showed up, carrying her divine staff and mirror shield with her. "All loyalty, but not very smart."
"Lady Palutena!" Pit bowed to Her Grace. "It's always an honor to serve you, Goddess of Light."
Palutena smiled warmly. "I'm always flattered that you feel that way! But alas, now's not the time for compliments. The Forces of Nature are once again up to trying to destroy the human race."
"Again?" Pit scratched his head. "How many times do we have to keep fighting them?"
"As long as their goddess Viridi continues to hate humanity the way she does, this cycle of fighting may never end," Palutena mused. "It's kind of a shame, too... We get along so well when we're not at each other's throats."
Pit smiled. "Yeah, I'll say; they're all really nice once you get to know them."
Palutena sighed at that. "Indeed... The only time we really had to get to know them better was when we all teamed up against the Aurum and the Chaos Kin. From what I saw, you and Viridi seemed to be becoming pretty close friends."
"She's actually really good company when she isn't being, well... Viridi."
Palutena giggled in response. "I might have even noticed a sort of connection between the two of you that even you and I don't have."
Pit's eyes lit up in confusion. "I'm sorry? I don't think anyone can come close to the loyalty between a captain of the guard and his loving goddess."
"Hehe. You'll probably find out later," Palutena teased. "Either way, I have a strange feeling about today..."
"What kind of strange feeling, Palutena?" Pit looked at her all serious. "Whatever it is, I'll be ready!"
Palutena shook her head. "You'll know when the time comes. It's just... I've got the strangest feeling that today will be a lot more hectic than usual. Be on your guard at all times."
Pit saluted his goddess and looked to his Centurions. "Everyone, you heard Her Grace! Be ready for anything today!" The soldiers all cheered and rallied together outside to prepare for the battles ahead. Palutena would soon follow.
"I just hope that feeling of mine is wrong. It feels as though the toughest battles of our life are just beginning..."
Author's Note
It actually really, really hurt me to recreate that scene from the movie. 
I hope I at least provided a good start.
But yeah, this is my new story. And yes, I'm crossing over with Kid Icarus: Uprising. For some reason, there wasn't even a tag for it. Can somepony fix that? 
