The following takes place between 10:00pm and 11:00pm

It's a relief seeing their pets unharmed. They decided to have them under ESCT protection. They're relocated in ESCT headquarters. After the break in, they increased security and changed protocol.

Rainbow Dash eyed on Brave Lance and Dark Spear. She had a bone to pick with them. The others can see she's filled with rage.

"Why did have to take over Wonderbolt Academy?" Rainbow Dash shouted.

"That wasn't us," denied Brave Lance.

"Tell that to Spitfire. She's devastated."

Dark Spear tried to calm her down. "Obviously Sect took siege of Wonderbolt Academy, pretending to be us."

"It's likely they'll use the Wonderbolts against us," theorised Twilight.

Jack rubbed his head. He remembered earlier, he and Rainbow Dash met one of them. He began to accept the way things work in the world of Equestria. He immediately jumped in on the conspiracy with Sect.

"Or probably they're weakening their defences," said Jack.

Some of the ponies didn't think it's possible. Jack explained more. "The Wonderbolts are like the air force. I think they're removing Equestria's defences, just to leave Ponyville and any other place, open for a surprise attack."

They couldn't find another reason for Sect's motive.

"The Wonderbolts aren't like the air force. They're an aerobics team," Rainbow Dash informed Jack.

"There's definitely a reason behind it," said Applejack.

"The Wonderbolts are not who you think they are." Pinkie became sneaky. "They could be working for Sect the whole time!"

Jack leaned to Applejack. "Does she always act that way?"

"You'll get the hang of her behaviour Mr. Bauer," Applejack answered.

Dark Spear hesitated, he believes that ESCT's compromised. He's hoping Brave Lance is thinking the same. "We should go and see Spitfire."

After going outside, Jack saw something appear on Twilight. Her wings flapped up and spread evenly. He's suddenly abashed. "You didn't tell me you're an alicorn."

"I've been using a spell that makes me look like a unicorn before I became a princess," explained Twilight.

"You miss being a unicorn?"

"A smidge."

He grabbed onto Twilight, while Fluttershy and Rainbow Dash waited for Rarity and Applejack to grab on. They immediately took flight. Pinkie Pie jumped and landed on Fluttershy. She felt a huge increase in weight.

10:19pm

Crates containing the items Sect need, stored in a warehouse, waiting for impending delivery. Handled by the Griffon Express. An inspector checked the boxes, he didn't find anything suspicious.

Underneath the supplies in the crates, were magical artefacts. They've been shielded to avoid them from going off.

10:22pm

A member of Sect, a unicorn named Lambda, inspected Tau for any trackers. He checked Omicron, Nu and Iota, they're all clean. He's surprised ESCT didn't bother try to find their hidden location.

"There's no need to use that disguise. They already know," Iota told Lambda.

Lambda created a light green cylinder barrier around him, transforming him into a changeling. "After that botched attempt at Shining Armour and Cadance's wedding, our faithful ruler disappeared. Thought it's an excuse to live the rest of the equines."

All of Sect are changelings. The one difference is they have letter of the Greek alphabet as cutie marks. They weren't part of Queen Chrysalis' plan of ruling Equestria. They're much older than an average changeling. They can change into different ponies, instead of impersonating a real one. They can choose their own appearances, type of equine, and their voices.

"Wonder why Alpha killed Beta," thought Nu.

"Good thing their feud has ended. Yet we still don't get what it's about. It's basically a secret agenda," answered Omicron.

10:27pm

Dark Spear immediately noticed what's been going on at Wonderbolt Academy. He spotted the ponies wearing similar uniforms. They didn't take notice of him or Brave Lance. None of them were concerned or taking notice of what's going on for past hour or so. Rainbow Dash was the first to arrive at Spitfire's office.

She saw Spitfire lying on her desk. She's using it as a place to sleep; she had nothing to do. She opened her eyes after hearing the door open. She's glad to see Rainbow Dash. When Brave Lance and Dark Spear came in, she prepared for an assault. Luckily Dash prevented her from charging.

"Before you make any sudden outburst, they did not take hold of the academy." Rainbow Dash raised her hooves as a sign of the two ESCT ponies not being a threat.

Spitfire spotted some differences with the armour Dark Spear and Brave Lance are wearing, and the armour the ponies wore when they occupied the academy. She controlled her temper, retaining herself from attacking them.

"They came to see why would members of ESCT came here, just to take hold of the academy," explained Rainbow Dash.

"I can tell by the uniform." Spitfire pointed to Dark Spear's getup.

Brave Lance looked at another armoured pony, noticing the oddities with his armour. He pushed them in the room, closing the door behind them. He spoke in a low, quiet voice. "You don't want to speak loudly, Sect's using the Wonderbolts to weaken Equestria's defences."

Spitfire didn't know what he's saying. She didn't see the Wonderbolts as a military force. There's clearly more to tell. She listened to hear more instead of trying to deny Brave's statement.

Jack told Spitfire about Sect's reason for using Wonderbolt Academy. "We believe it is Sect's first step."

"Step in what?"

"We do not know, but we believe they want to weaken Equestria."

Pinkie Pie jumped in. "You don't have to worry, we got a human who can help you."

Jack felt frustrated with Pinkie exploiting his duty. The hysteria is what prevented him from restraining any pony. He wished it will end.

"How are we going to get rid of the problem?" Spitfire asked.

"We need to find the others," said Rainbow Dash.

"Soarin and Fleetfoot are in the detention cells. They rebelled against the changes Sect made."

"And I thought I was the hot-headed one."

Jack looked at the map of the entire academy. He peeked out the door and window. "I have a plan and it's going to involve all of you."

Derpy arrived at the front door. She knocked at the door. One of the impersonating ponies answered.

"Letter for Spitfire," Derpy said in a polite voice. "Also a package for the Wonderbolts."

The pony took both letter and package. When asked to sign, he used a fake name. Derpy flew away and just as she descended, she covered her ears with her hooves.

Instead of giving the letter to Spitfire, he opened it and read it. "Do not open the package. How mundane is that."

He brought it over to the Soarin and Fleetfoot, the other Wonderbolts were in the cells as well. He hands Soarin the package. He shook it; he first thought it's a pie, he wanted to break out so bad, that he didn't raise any hopes.

"Any idea what's in it?" asked Fleetfoot.

"We'll just see." Soarin ripped it open.

Gas masks and a piece of paper were inside. Fleetfoot read it. "In about ten seconds after reading this, we'll be setting up bust. Use the shackles on the bars and apply the masks."

They tossed the masks and put them on. Once they counted down to one, when smoke grenades flew in. Rainbow Dash and Fluttershy used their wings to spread the smoke, aided by Cloudchaser and Flitter.

Pinkie Pie used her party cannon to stun the ponies from Sect. Applejack charged, knocking them down like bowling pins. Twilight and Jack entered wearing gas masks, trying to find the keys to the cells. They managed to free them and entered the main hall.

After the smoke cleared, all of the Mane 6 rejoined, along with Cloudchaser and Flitter.

"Good job every pony," said Spitfire.

Applejack looked at Jack. "How did you know that smoke grenades will work?"

"He's worked for CTU for years. He knows this stuff," said Rainbow Dash. "It's also nice to see Rarity use magic besides for creating fashion."

"Why choose Rarity?" Twilight asked. "I more experienced with magic."

Rarity smiled. Jack persuaded her to tell. "It wasn't easy. Jack gave me a description of what he needed. He thought I should be given a chance to try something out of my comfort zone."

"At least got the Wonderbolts…" Rainbow Dash only saw Spitfire, Soarin and Fleetfoot. "…three of them?!"

The rest of the Wonderbolts stood still, staring at them. They were giving evil smiles and their eyes were glowing. The imposing ponies trotted in, they have control over them. Rainbow Dash noticed something suspicious. She looked at one of them. She pounded one on the head with her hoof, causing its disguise to wear off.

"Changeling!" she exclaimed.

They rest changed to their original forms. Jack can see he and the ponies are outnumbered, he slowly reached for his gun. Even though he doesn't have enough bullets to kill them all, he wasn't planning on shooting them. He came up with a different plan. He unlinked a belt with the last of the smoke grenades. Instead of pulling the pins, he put his gun on one, while keeping the rest in straight line.

"When I give the word, run," Jack told Spitfire.

The changelings were ready to attack. The brainwashed Wonderbolts were ready too. Jack placed his finger on the trigger. "Go!"

He fired around, exploding all the grenades creating a cloud of smoke. Jack ran out of the academy and grabbed onto Spitfire. Soarin carried Applejack, Fleetfoot carried Rarity and Pinkie Pie jumped on Twilight Sparkle. Rainbow Dash and Fluttershy chose Brave Lance and Dark Spear.

Spitfire marched to Jack. Instead of thanking him, she threw a fit. "Explain why we had to retreat. We could have taken them-"

"There were too many of them," interrupted Jack. "If they capture us, we won't be able to determine Sect's motive for ruining Equestria."

"He's right," said Rainbow Dash. "We need a plan."

"How did you know they were changelings?" Spitfire asked Dash.

"We had a run-in with them at a wedding."

She told her about the changeling invasion at Cadance and Shining Armour's wedding.

"I think I should tell you that the changelings who are part of Sect, are your typical changelings," added Rarity.

"You're right," agreed Fluttershy. "The changelings from Sect have their own voices and can change into different ponies rather than duplicating."

"Any word on the changeling queen?" Spitfire asked.

"I appears she and her army might be under their grasp," theorised Jack.