With Sonic grabbing Sunset, they met up with Twilight and Amy at the abandoned Eggman base in Echo Mine.

"Y'know what I like best about Eggman?" Sonic asked.

"What's that?" Sunset asked.

"His subtlety. It looks like it was a heck of a battle here."

"There was!" Amy exclaimed. "This was where one of the biggest counter-attacks on Dr. Eggman's forces happened before you come back to us."

"We were able to liberate a lot of people that day, " Twilight said as drop to ground level. "In the process, we lost a lot of good people and ponies too."

"Hey, you sure made it worth it," Sonic came to the alicorn's side.

"You won the war for us."

"Well, yeah, saving the day is what I do."

"And stop him from performing his encore," Sunset said. "Which way?"

"The command hub is down this tunnel, hopefully, the backup generator still works," Amy said. "With some luck. we'll be able to boot the computer his computer access his networks and find out what's he's up to!"

"Sliver, Pinks, and Crash saw his badnik emptying out a defect lab, though how do you he's not doing the same thing?"

"I don't, but this is the closest abandoned base on file, so this is the best place to start!"

The quartet arrives at the command hub and reactivates the power in the Echo Mine once Amy finds the backup generator.

"We're in business!" Amy exclaimed.

"Damn, not even reserve badniks? Snore-Fest." As Sonic was disappointed not to find any Badniks.

At the Final Egg. Eggman, Orbot, Cubot, and Cozy were putting his Metal Virus in containers.

"This is so mean, I almost feel bad for those dopes, almost." Cozy grinned then Starline and Chrysalis enter the room.

"Sir! There was a ping on the Eggnet!" Starline exclaimed. "The Echo Mine has come back online!"

"Kay and why should be concerned because...?" Eggman asked.

"Because, Sonic, Amy, Miss Sparkle, and Miss Shimmer have unguarded access to your files."

"What perfect timing! Cubot. tell Rough and Tumble to meet me in Hanger three, you and Chrysalis make sure everything is ready for phase two."

"You got boss!" Cubot said as he went ahead.

"How can you be so casual about this? The Metal Virus may be viable, but you haven't finished-"

"Starline," Eggman interputed him. "You need to learn to enjoy these dramatic sudden deadlines."

Sometime later, Eggman, Orbot, and Starline met up with Rough and Tumble with Rough kicking Cubot's head.

"You finally get off your fat but and get us those weapons?" Rough asked.

"We got half a mind to take over this dump for ourselves," Tumble said.

'Half a mind is being generous.' Eggman said to himself then gave the Metal Virus backpacks. "These are your backup, in case sonic gets the upper hand."

"Are these superpowers or something?" Rough asked. "If these are these are back-ups what're we leading with?"

"Get a load of this!" Eggman reveals his latest invention making the skunk brothers delighted.

Back at the Echo Mine Base.

"Pony feathers, login screen," Sunset groaned. "Please you his passwords."

"One second," Twilight told her then enter the login and gain access. "I'm in."

"Nicely done," Amy thanked the looked for the most recent files showing the blueprint of s for a contraption.

"Is that the Space Colony Ark?" Sonic asked.

"No, this looks too much smaller. I'm seeing a lot of talk about 'payload' but of what...?"

Before they can learn more the computer shuts down.

"Crap! We need to know more!" Amy fret.

"I think Eggman just remembered his forgotten base!" Sonic exclaimed then Rough and Tumble bargein while driving dril-based tank.

"We'll cave in the mines!"

"Bury you in the rubble!"

"You gonna get wrecked by Rough and Tumble!" They introduce themselves with their usual showmanship and rhymes.

"Hey dumbasses, " Sonic called them. "If that's going to be your thing, it needs to rhyme!"

"We did rhyme! Sort of..."

"How did in the hell, those guys were able to take over a whole town?" Sunset asked Twilight.

"Completely dimwitted, but still dangerous," Twilight told while both of them charged their horns. "Let neutralize the drill, first!"

"Got it!" Amy swung her hammer only to be propelled backward without leaving so much as a dent.

"Screw it!" Tumble said. "We'll steal a rhyming dictionary later!"

"Right!" Rough agreed. "We've got roadkilled to serve up!"

Rough and Tumble decide to focus on their targets and begin shooting at the hedgehogs and the mares.

"Hold on tight!" Twilight said. "I teleport out of here!"

Twilight teleported them out of the line of fire.

"Where the hell did they go?" Rough asked.

"Could've gone that far," Tumble said as they moved.

Twilight teleported all of them to safety and then look around their surroundings.

"Where are we?" Amy asked.

"Dead end," Sonic suggested.

"It's a refuse pit!" Sunset said. "The only way out is back the way we came!"

"Hold on, this path is barely enough for their tank," Twilight thought. "If they drove out here they wouldn't be able to turn around. Allowing us to attack from behind."

"You don't say," Sonic smiled as he, Amy, and Sunset liked the plan.

"End of the line, suckers!" as Rough and Tumble crash through the entrance.

"Hard right, Rough!" Tumble exclaimed.

"Oh crap!" Rough exclaimed making a hard right turn when they nearly drive straight into the pit.

"You know Twilight, I almost feel bad for what we're about to do, almost!" Sunset said. "Are you guys ready?"

"We're set here!" Sonic used his speed to run up behind the tank.

"Damn it!" Tumble shrieked. "We're surrounded."

Sonic threw Amy overhead and landed on top of the tank and Twilight flew to her and Amy brings her hammer.

"No, no, no!" Both Twilight and Amy attacked Tumble's glass pod then Sonic did a Spin Attack which got enhanced by Sunset's magic blast destroying the tank's left treads.

"Bail, Bail!"

"Why didn't gives flamethrowers!? Or goddamn bazooka?! Not this bug dumb tank!" Both got out of the tank and got cornered!

"It's over you two!" Twilight charged her horn. "Tell us where is Eggman is and we'll go easy on you!"

"Joke's on you, toots!" Rough said.

"We've been saving the big guns for last!" Tumble added as they engaged their backup plan, pressing the buttons on their cross-straps as instructed. However, this only causes the backpacks to open up, spilling the Metal Virus onto both of the skunk brothers.

"What in Equestria is that!?"

"No idea."

The duo panic as the liquid engulfs them, destroying their backpacks as their bodies become metallic.

"They're robots! Not badnik, but..." Amy was horrified.

"Something way worse!" Sunset grimly said as both attacked. "Look out!"

The skunk bros attacked as Tumble chased after Sunset and Sonic, and Rough went for Amy and Twilight.

"Honestly though? It's a good look you, More 'sports car' less 'haven't washed in a week!" Sonic tries to agitate Tumble with insults, but the skunk ignores him as he presses his attack.

"Neither are responding! It's like they're completely soulless!" Sunset exclaimed.

"Eggman somehow turned them into Zombie Bots," Twilight said while fending off Rough's attacks. "So... Zombots?"

"Really, Twi?" Amy asked her.

"I like the name... it works!" Sonic exclaimed.

"Thanks!" Twilight did a magic blast and Amy swung her hammer tearing off his left arm and leaving a deep gouge in his body.

"Oh my gosh! I'm sorry! I didn't know that would what the hell?!" Amy was mortified then Rough quickly regenerates. "Guys! I don't think we can hurt them!"

Sonic did multiple Spin Attacks at Rumble and Sunset forward the pressure and did Sunset Burst at him only for the brute to restore the damage within seconds.

"I think your right, Amy," Sunset then had a horrifying look at Sonic. "Uh, Sonic..."

"Yeah..." Sonic wiped his mouth and realizes that the Metal Virus liquid was on his hand after having touched Tumble. "Amy! Twilight! Sunset! Don't let them touch you!"

Tumble gut-punched him then Sonic tossed him into a pit then kicked Rough into a pit as well.

"It's a bit rough than I want to play it but I'm kind of in trouble," Sonic exclaimed as his body is now covered in metallic patches. "Whatever changed them is infectious. So any idea? Cause this is spreading Fast!"

Meanwhile Cozy, Chrysalis, and Shadowforce watch the event unfolds.

"Good news, doc!" Cozy contacted him. "The hedgehog is infected and got to hand to him it's catchy."

"I suppose, it works, shall we move to phase two which is..." Shadowforce started.

"Disturbing the Metal Virus through the world! The end is here for them!" Chrysalis laughed then Cozy join her.

Shadowforce is an OC of mine that made an appearance in the 7th season finale of MLP FIM
After defeating the Pony of Shadow, a small part of his magic was formed into a being of mass destruction and joins the ranks of Tirek, Cozy, and Chysails to bring an end to all ponies.

Artwork supply by Venjix5