Author's Note: Well after doing somethings I can finally give you the next chapter. But I'm sure you don't want to hear it so here's the next chapter.
Chapter 3: I Was Having Twelve Percent of a Moment
Doctor Whooves is talking with the Council, four shadowy figures on screens. "This is out of line, Director. You're dealing with forces you can't control."
"You ever been in a war, councilmare? In a fire fight? Did you feel an over abundance of control?" Whooves said.
"You're saying that this Canterlot is declaring war on our planet?"
"Not Canterlot, Trixie." he corrected.
"She can't be working alone. What about the other one, her sister?"
"Our intelligence says Twilight is not a hostile. But she's worlds away and we can't depend on her to help either. It's up to us." the brown pony said.
"Which is why you should be focusing on Phase Two, it was designed for exactly this purpose."
"Phase Two isn't ready, our enemy is. We need a response team." he told them.
"The Avengers Initiative was shut down."
"This isn't about the Avengers." he said.
"We're running the world's greatest covert security network and you're gonna leave the fate of the pony race to a handful of freaks."
"I'm not leaving anything to anyone. We need a response team. These ponies may be isolated, unbalanced even, but I believe, with the right push, they can be exactly what we need." Doctor Whooves explained.
"You believe! War isn't won by sentiment, Director."
"No, It's won by soldiers." Whooves said leaving them.
Meanwhile
In a gym Applejack is hitting a punching bag. But while she was hitting it she was having flashbacks about her past.
"There's not enough time. I gotta put her in the water."
She hits the bag harder and even faster.
"You won't be alone."
She then hits the bag even faster.
"Oh my God. This pony is still alive."
She turns 180 degrees throws the hardest buck with the back of her hooves and sends the bag flying against the wall. Breathing hard, Applejack picks up another bag from a line on the floor and hangs it up to hit it.
"Trouble sleeping?" Doctor Whooves asked across the room.
"Slept for seventy years, sir. I think I've had my fill." she said as she hit the bag.
"Then you should be out, celebrating, seeing the world." he said coming closer to her.
"When I went under, the world was at war. I wake up they say we won. They didn't say what we lost." she said removing the wraps on her hooves.
"We've made some mistakes along the way, some very recently." he said.
"You here with a mission, sir?" she asked.
"I am." he replied.
"Trying to get me back in the world?" she asked.
"Trying to save it." he responded
Whooves then hands Applejack a folder with information on the Tesseract in it. "Hydra's secret weapon." she said.
"Howard Dash fished that out of the ocean when he was looking for you. He thought what we think. The Tesseract could be the key to unlimited sustainable energy. That's something the world sorely needs." Hooves explained.
"Who took it from you?" the orange pony asked.
"She's called Trixie. She's...not from around here. There's a lot we'll have to bring you up to speed on if you're in. The world has gotten even stranger than you already know." he said.
"At this point I doubt anything would surprise me." Applejack said getting up, grabbing her duffel bag, and another punching bag while Whooves is talking.
"Ten bits says you're wrong. There's a debriefing packet waiting for you back at your apartment. Is there anything you can tell us about the Tesseract that we ought to know now?" Hooves asked.
"You should have left it in the ocean." Applejack said before she was gone.
Meanwhile (again)
We find Iron Dash underwater attaching a device to a massive pipe. She then flies up out of the water and towards the city. "Good to go on this end. The rest is up to you." she said to her assistant.
"You disconnected the transmission lines? Are we off the grid?" Scootaloo asked.
"Dash Tower's about to become a beacon of self-sustaining clean energy." she explained.
"Well, assuming the arc reactor takes over and it actually works." the assistant asked.
"I assume. Light her up." Dash ordered heading towards her tower. And after a while Dash Tower starts to lights up.
"How does it look?" Scootaloo asked.
"Like Christmas but with more...me." Rainbow Dash explained.
"We've got to go wider on the public awareness campaign. You need to do some press. I'm in Fillydelphia tomorrow. I'm working on the zoning for the next three buildings-"
"Scootaloo, you're killing me at the moment. Remember, enjoy the moment." Dash said.
"Then get in here and I will." the assistant said. Iron Dash then lands on the landing pad of the tower and walks along a walkway while robotic arms deconstructing her armor.
"Ma'am, Agent Spike of Time is on the line." her computer JARVIS said.
"I'm not in. I'm actually out." she told her computer
"Ma'am, I'm afraid he's insisting." JARVIS said.
"Grow a spine, JARVIS. I got things to do." she said heading inside. Scootaloo is standing in front of a holographic display, a little confused.
"Levels are holding steady...I think." Scootaloo said. Dash then approaches her.
"Of course they are, I was directly involved." Rainbow said as she turns off the display and Scootaloo and her face each other. "Which leads me to my next question. How does it feel to be a genius?"
"Well, ah, I really wouldn't know now would I?" the assistant replied.
"What do you mean? All this came from you." the blue pegasus said.
"No, all this came from that." she said pointing at Rainbow's arc reactor.
"Give yourself some credit, please. Dash Tower is your baby. Give yourself...twelve percent of the credit." the pegasus with the destroyed wings said.
"Twelve percent?" the assistant said.
"An argument can be made for fifteen." Dash said as Scootaloo walks toward the living room.
"Twelve percent of my baby?" the assistant asked.
"Well, I did do all the heavy lifting. Literally, I lifted the heavy things and sorry but, the security snafu? That was on you." Rainbow explained following her.
"Oh!" the assistant said understanding.
"My private elevator-"
"You mean our elevator." the assistant said.
"Yeah, it was teeming with sweaty workponies...I'm going to pay for that comment about percentages in some subtle way later aren't I?" Rainbow asked.
"Not gonna be that subtle." the assistant said.
"I'll tell you what, next building is gonna say Scootaloo on the tower." Dash said.
"On the lease!" Scootaloo said.
"Call your mom, can you bunk over?" Dash asked.
"Ma'am, the telephone. I'm afraid my protocols are being overridden." JARVIS said. Dash then picks up her high-tech phone and holds it up.
"Ms. Dash, we need to talk." Spike said through the phone.
"You have reached the Life Model Decoy of Rainbow Dash. Please leave a message." she said.
"This is urgent." the dragon said.
"Then leave it urgently." she said. The elevator then opens and Spike comes out. "Security breach...That's on you!" she said to Scootaloo.
"Spike! Come in!" Scootaloo said as she and Rainbow Dash both walk over to Spike.
"Spike? Uh, his first name is Agent." Dash said.
"Come on in, we're celebrating." Scootaloo said.
"Which is why he can't stay." Rainbow said. Spike then hands her a laptop.
"We need you to look this over, as soon as possible." Spike said.
"I don't like being handed things." she told the dragon.
"That's fine because I love to be handed things." Scootaloo said taking the laptop from Spike. She then passes it to Rainbow Dash.
"Official consulting hours are between eight and five every other Thursday." Dash said going to other side of the room.
"This isn't a consultation." Spike said.
"Is this about the Avengers?" Scootaloo asked making Spike look at her. "Which I know nothing about."
"The Avengers Initiative was scrapped, I thought, and I didn't even qualify." Dash told her.
"I didn't know that either." Scootaloo said.
"Yeah, apparently I'm volatile, self-obsessed, don't play well with others." Rainbow said checking out the laptop.
"That I did know." the assistant said.
"This isn't about personality profiles anymore." Spike said.
"Whatever! Scoots, got a sec?" Dash asked.
"Hold on a moment." Scootaloo said leaving Spike at the door as she goes over to Dash.
"You know, I thought we were having a moment." Rainbow said.
"I was having twelve percent of a moment." the assistant said. "This seems serious. Spike looks pretty shaken."
"How would you notice? Why is he Spike?" Dash asked.
"What is all this?" Scootaloo asked.
"This is ah..." Rainbow Dash then grabs the holograms on the laptop and throws them up and they fill the room showing Applejack, Fluttershy, Twilight, Pinkie, and Rarity in action. "...this!" The ponies both look upon the screens, observing them.
"I'm going to fly over to Fillydelphia tonight." Scootaloo said.
"Tomorrow." Dash said.
"You have homework. You have a lot of homework." Scootaloo said.
"Well, what if I didn't?" Rainbow asked.
"If you didn't? You mean when you finished? Well, um, then..." She then leans in and whispers in Rainbow Dash's ear.
"Square deal. Fly safe." Rainbow Dash said.
"Work hard." Scootaloo said leaving.
"So, any chance you're flying by LaGuardia?" Spike asked.
"I can drop you off." Dash said.
"Fantastic. Ooh, I want to hear about the ah..cellist, is that still a thing?" Scootaloo said. Rainbow Dash then sees the Tesseract and becomes interested.
"She moved back to Tartarus." Spike said.
"What?...Boo." Scootaloo said before she was out of the room.
Author's Note: Well I hope you enjoyed that. Also I want to explain something. Scootaloo is pretty much Rainbow Dash's assistant but they really have a big sister little sister relationship. So tune in next time for the next chapter.