Ponyville, Equestria

Around Midday

Twilight Sparkle, Princess of Equestria, could be described as very attentive to things. However, she was so focused on her annual report to Celestia, she didn't even noticed her Cutie Mark was glowing until it was noticeable in her peripheral vision.

"Spike!" she cried upon seeing the glowing light. "Get the girls!"

"They're already here!" the baby dragon replied. Twilight headed for the Cutie Map, and she smiled upon seeing her friends already sitting down.

"Where to?" Rainbow asked. "and who's going?"

"No clue as of yet." Twilight asked, activating the map. To everyone's surprise, the cutie marks of all six Elements were shown. The map moved in on Ponyville, into Twilight's Castle, and then…

It stopped on the Mirror Portal.

"Twilight…" Applejack asked. "The map's sending us through the portal?"

"I think so." Twilight said, still as shocked as could be. "That's never happened before. Lemme check with Sunset, see if she's okay."

Twilight brought out her Journal, and wrote.

"Sunset, everything alright in terms of Friendship problems over at the school?"

The reply took several minutes to appear.

"Yes, but I'm in class, Twilight, and I'm risking a detention. What's up?"

"Friendship Problem that's apparently through the portal", Twilight wrote. "Advice?"

"Can't say I have any." Sunset replied. "Got to go. Mrs. Lightwood is collecting papers."

Twilight put the journal away, and sighed.

"Guess we'll find out when we go through the portal." she sighed. "We all ready?"

"Ready as we'll ever be." Fluttershy said.

"Let's go!" Rainbow cried. Twilight led them to the portal, and with a blast of magic, changed the destination to the location of the problem. The six of them entered, and they were gone in a flash of white light.

====
Brooklyn Airstrip
New York

SHD Agent Nick Sykes stood on the helipad, watching the sun rise on Manhattan in the distance. He heard footsteps, and he looked over his shoulder to see three other SHD agents walk up. He recognized them through their SHD Tags on their wrist and shoulder as the agents assigned to his team, designated Team Sierra-Kilo.

Logan Johnston, a Sniper. He was armed with a Hunting M40 Marksman rifle.

Harper Andrews, a Combat Medic. She was equipped with a Navy MP5N submachine gun.

And Kyle Ralston, a Support gunner. He carried a FN-MAG 50 machine gun. They all wore typical urban or suburban clothing, and from what Nick could see, they were activated around the same time as he was. Nick looked back at the weapon he carried, a Custom P416 assault rifle. Kyle approached and tapped him on the left shoulder, then he smiled.

"Morning." Kyle said. "You're Agent Nick Sykes?

"Yeah." Nick replied. "You and the others are teaming up with me, I suppose."

"You suppose right." Harper said. "Let's get to it, I guess."

"Let's, indeed."

The four agents turned to see Faye Lau, the Second Wave agent they all had met earlier, come up to stand next to them.

"Yeah, when we're all done here, I'll buy drinks." she smiled. "I know a place that serves the best Whiskey Sours in Manhattan. On me, if...when we take this city back."

The agents shuffled, knowing their work was cut out for them. The roar of engines turned their heads to the incoming V-22 Osprey Helicopter approaching the landing pad.

"The rest of us should be in this chopper." Lau said with excitement. "Can't believe it's finally happening."

The five of them approached, and the Division Commander lowered the door.

"Welcome Agent!..." was all they heard before the Helicopter exploded in a bright orange fireball. The four agents were knocked out, and Lau was blasted away, shrapnel tearing into her right leg.

====

Nick awoke to a hard smack to the back of the head. He sighed groggily as he opened his eyes, revealing the mid-morning Manhattan skyline..

"Wake up, I need you!" Lau said, injecting a Medkit into his chest. Nick turned to see he and his fellow agents were in a large-cap civilian helicopter. Nick could also see Lau's heavily bandaged face and leg.

"Look, you're all going to be okay." Lau said, groaning. "More okay than me, but...shit. That explosion took out the commander. And we still have a job to do here. And we're still going to do it!"

"That's for damn sure." Logan said, pumping the air. Lau sighed, and looked at Nick.

"Look, I found out more about the First Wave. They're all either dead, or MIA. So this is up to us, and we need to get it together. Right. Now."

As the pilots talked over the radio, Lau handed each Agent a Sidearm from an ammo crate.

"Usually you need time to know if you can count on someone, but we're out of time." she said. "My bet's on you four. I'm hoping to god I'm right about this."

The four mobile agents disembarked as the Helicopter landed. While Lau talked with the two JTF medics on site, Nick motioned for his team to head for the Camp Hudson gate. The JTF gave them a "Good luck!" before they set off.

====

They didn't get very far before ISAC spoke with an urgent message.

"Warning, detecting radiation and atmospheric electrical activity!"

"What's going on?" Nick asked.

"And what's that?" Harper asked, pointing to a glowing ovoid vortex that was growing in front of them. The Agents slowly advanced, with weapons ready and loaded. Then, there was a terrific blast, and the agents were thrown to the ground, their vision blinded. Nick groaned, and he could hear female voices speaking loud and clear..

"We made it!" said a bright and cheery voice. "I should throw a party!"

"A party?" Nick thought, still unsure of what happened just then.

"I think we've got bigger problems, everypony." said a more refined voice.

"Everypony?" Logan thought with disbelief. Their vision returned to normal as Logan and Harper helped Kyle and Nick to their feet. And what Nick saw shocked him flat. Six multicolored equine creatures, along with a smaller, lizard-like one were piled in a heap on the dock, and apart from their speaking understandable English, they were also getting their bearings and trying to stand up.

Then the JTF raised their weapons and advanced on them. One with a yellow coat and wings whimpered, another with wings and a rainbow-colored mane growled ferociously, and the various others had solid fear on their faces. The lizard clung ot the purple one like a scared child. The SHD Agents had seen enough by this time, and they walked towards them.

"JTF!" Nick said, drawing the attention of the soldiers. "Stand down. We got this."

The JTF Soldiers stepped back, though their various Police M4 and Super 90 shotguns didn't lower from their potential targets. Nick and his team walked towards them, and Nick did something, something that he had no idea how they'd respond to.

He extended his hand, offering to pull a lavender one with a horn and wings to her hooves.

"It's okay." he spoke in the kindest tone he could muster. "Nice of you to drop in."

====

Even though Twilight knew it was a bad attempt at humor, she chuckled and placed her hoof in the human's outstretched hand. She was pulled up, and she could see the other humans relax visibly.

"I guess we should introduce ourselves?" she asked the human, who nodded.

"Later." he said. "What are you?"

"I'm an Alicorn pony." she said.

"Well, I've never seen a pony who's purple." the human said.

"It's lavender." she said. "And it's a long story."

"Tell us, then." another human, a female, said as she approached. "We've got time for a story."

Twilight saw two other humans approach.

"Alright, but it'll be a while." she cautioned.

"We'll be alright." the leader said. "Soldier, where's somewhere private we can go?"

"The depot, I guess." the soldier replied. "Just...keep them away from the civilians. We don't want another outbreak of some alien sickness here."

"Roger that." Nick said. As the four of them escorted the six ponies and a noticeably nervous lizard away, with the pink one bouncing instead of walking, they didn't notice a small drone monitoring them through a camera. Marked with a Deer-skull logo, it buzzed off towards the southern part of Camp Hudson, away from the JTF.

Author's Note

Yep, this one's gonna be GREAT!

This story will follow the rudimentay mission order I have set up. It goes Rioters, then Cleaners, then Rikers, then LMB. Dark Zone will be towards the end, and Underground and Survival will come later.

Also, I will make a spreadsheet with Agent gear and skills to post here later.
EDIT-Here is the Roster

Do you like the start?

EDIT 2-Added in Spike.