This takes place after "The Royal Wedding" from MLP:FiM and sometime around the end of the fourth season and into the fifth season of Winx Club. Just so you know the timeline I'm working with. Enjoy it!

Chapter 1: A Harsh Reality

In the not too distant future, is a land that was called Equestria. The once beautiful landscape was now reduced to a barren wasteland, nearly devoid of life. The Changelings and other unknown creatures swept across like a swarm of locusts led by their Queen. Princess Celestia and Princess Luna with their armies did their best to fight but were quickly overcome due to the Queen and her subjects newly obtained powers. Rumors spread that three witches came to Equestria and formed an alliance with the Queen to take over everypony. A resistance soon developed led by the last remaining royal pony, Princess M'Amore Cadenza, or Cadence to her friends. In their secret base, Cadence was going over their history database that Twilight Sparkle helped put together to see if there was anything she might have missed to help them defeat the Queen and her witch allies. The door opened and Applejack came galloping in.
"Princess Cadence! Manehattan has been taken by the Queen's forces!"
"What?! Are you sure dear Applejack?"
"As sure as apples grow on trees."
"What are the casualties?"
"Half of Rainbow Dash and Soarin's armies were takin' out. A few survivors managed to escape but we don't know where to take them."
"And what of Rainbow Dash and Soarin'?"
"They're in the infirmary now."
Cadence looked crestfallen; at this rate, they'll all be wiped out. Manehattan was one of the few cities they had, now Ponyville and Canterlot and Cloudsdale are all that remain.
"Applejack, I want you to take the remaining survivors and divide them up to go to Ponyville, Canterlot and Cloudsdale. Make sure you stop by Rarity's supply store and make sure they all have what they need."
"Yes, Your Highness."
Applejack bowed and left the room. Cadence returned to the screen to study some more.
"There has to be something here; something that could give us some sort of clue."
Meanwhile, Applejack was at Rarity's shop making sure the survivors are getting necessary supplies.
"These poor folks have been through so much," said Applejack.
"Yes, these poor dears," said Rarity.
"Rarity, you are needed at the front," said Fancy had lost his wife and home during the first rounds of attack. He then quickly became Rarity's partner to help her disperse supplies to those who needed them.
Rarity made her way to the counter while Fancy Pants and Applejack continued to talk.
"I do say, there seems to be a few more survivors than from the last attack," said Fancy Pants.
"They have Rainbow Dash and Soarin' to thank for that. From what I understand, their army took the brunt of it so more ponies could get away. The Princess sure does appreciate you using your resources to help us out."
"It is the least I could do."
"Fancy Pants! Come here quick," cried Rarity.
Both Applejack and Fancy Pants raced to the front to see what had Rarity screaming. They saw Rarity standing next to a blue coat and white mane mare with a lace doily cutie mark with her two children, a filly and a colt. Fancy Pants' eyes went wide.
"It cannot be," he said.
"Fancy Pants! You're alive," cried the mare. "Dear brother, I've been so worried about you!"
"Frilly! My dear sister! But where is your husband Orion?"
Frilly looked down and the young ones began to cry.
"He didn't make it. He fought off the Changelings so we could get away."
"Oh dear Frilly, you and the children can stay here in Ponyville. Applejack, could you please make sure they get a place in Ponyville," said Rarity.
"I'll see what I can do," said Applejack.
Back at the infirmary, Fluttershy came to check in on Rainbow Dash and Soarin'.
"Excuse me nurse, how are the patients doing?"
"They're healing quite nicely. They've actually awaken now."
"Oh, thank goodness. May I see them?"
"Since it's you, I suppose that would be alright," said the nurse pony.
As the nurse led Fluttershy to see them, a familiar pink pony came bounding up behind them.
"Hey Fluttershy! Are you going to see Rainbow Dash? Cause I heard they were going to be ok so I hurried over here but not before I planned a Get Well Soon party for them! It's going to be great! There's cake and punch and games and music! You think they'll like it? I know I would!"
As she began to ramble on, Fluttershy gave her a stern look to get her quiet. Pinkie Pie then acted like she was zipping her lips. They got to the room and opened the door; Rainbow Dash was sitting up while Soarin' stood next to her bed.
"Why are you out of bed Soarin'?! You still haven't fully recovered," cried the nurse.
"I'm fine, I'm just making sure Rainbow is fine."
"I'm ok, it's you who got seriously hurt. You didn't have to take that hit for me."
"What kind of husband would I be if I don't protect my mare?"
Rainbow Dash blushed at the remark. She still never got used to that kind of talk. She then saw her two friends at the door.
"It's nice to see you guys; where's Applejack," asked Rainbow Dash.
"She's getting the survivors settled at the request of the Princess," said Fluttershy. "Those ponies have you two to thank for saving them. From what I hear, it would have been a lot worse without you."
Rainbow Dash noticed Pinkie Pie was being unusually quiet.
"Hey Pinkie Pie; you got anything to eat? The food here is terrible," said Rainbow Dash.
Pinkie perked up and brought out cupcakes for everypony.
"I baked these especially for you! I hope you can come to your Get Well Soon party I planned for you! It's going to be great! There's cake and punch and games and all kinds of fun!"
"Pinkie," cried Soarin'. "We'll be there."
Pinkie then began to dance around until three notes appeared before them. Rainbow Dash read hers aloud.
"My dear friends, it is urgent that you come to the base at once. I believe I have figured out a solution to destroy the Chrysallis armies and return peace and balance to Equestria. Signed, Princess Cadence."
"Oh my, what do you think that solution is," asked Fluttershy.
"Whatever it is, it's important for us to hear. Let's go everypony," said Soarin'.
Back at base, Fluttershy, Pinkie Pie, Rainbow Dash and Soarin', along with Applejack, Rarity and Fancy Pants stood before Princess Cadence with the screen behind her.
"My friends, I have called you here because you are the group of ponies I trust the most. I have been pouring over this screen to figure out where and how the Changelings managed to take over. That answer was not found within our pony history. So I did a search of other histories from across the universe, and this was what I saw."
An image of the Changeling Queen making a deal with a white haired, dark blue attired woman and two other beings one with frizzy hair and magenta clothes and the other with dark brown hair and purple clothes laughing maniacally. The other ponies gasped in fear.
"So the rumors were true! They did receive help from witches," cried Applejack.
"They are called Icy, Darcy and Stormy. Very formidable and deviously wicked," said Cadence.
"But why couldn't you and Shining Armor just repel them like the last time," asked Fancy Pants.
"Because, they were infused with an even stronger and darker magic. Our strength alone wasn't going to be enough," said Shining Armor as he came in from the back.
"Not even Princess Celestia and Princess Luna were powerful enough to stop them. But, I have also discovered how we can beat them. These three witches have very powerful enemies. They are known as the Winx Club." An image of the Winx Club in their Harmonix fighting the witches appeared on the screen next.
"So we're gonna go find this Winx Club and ask them to help us," asked Fluttershy.
"What I have devised is this. We send somepony back around the time the Changeling Queen and the witches meet and beseech the Winx Club to come to Equestria and help defeat them so that this horrible nightmare will never come to pass," said Princess Cadence.
"I'll go Your Highness," said Soarin'.
"No, I'll go," said Rainbow Dash.
All the other ponies volunteered themselves but Princess Cadence silenced them.
"I appreciate your bravery, but I have already chosen and sent our champion," said Princess Cadence. Suddenly, the alarm began to sound. Cheerilee and Big Mac came running in with the Cutie Mark Crusaders behind them.
"Princess! The Changeling Armies are on the attack," cried Big Mac.
"Where are they," yelled Shining Armor.
"On the outskirts of the Everfree Forest! Zecora confirmed it," said Apple Bloom.
"Soarin'! Rainbow Dash! I can't ask you to risk your lives for us again. Applejack, Big Mac; take every able bodied pony with you to fight them off," said Princess Cadence.
"With all due respect Princess, but we can't just stand by and do nothing," said Soarin'.
"We'll gladly lay our lives down for Equestria," said Rainbow Dash.
"Me too," said Pinkie Pie.
"And me," said Fluttershy.
"Us as well," said Rarity and Fancy Pants.
Princess Cadence was moved by everyponies bravery. She agreed to let them go and as they left, she returned to her screen.
"Please hurry; we're all counting on you."