When the sun rose across the land of Equestria, everypony was getting up to start a new day. At Twilight's castle, both Ben and Rook had been given their own temporary bedroom during their stay in Equestria.
In Ben's room, the teen was sleeping until Spike entered and spoke up, "Uh, Ben, it's morning."
Ben woke up and sat up in bed before looking at the young dragon, "Thank you, Spike."
"Wow. From the way Rook talks about you, I thought you'd wake up cranky or something." Spike said in surprise.
"Rook tends to exaggerate the most." Ben answered, as he got out of bed, "Besides. I'm used to having someone wake me up in the morning."
"You are?" Spike asked, "Well, that's cool I guess, come on, everypony's having breakfast." Spike said, as the two walked towards the dining hall.
When the two entered the room, they saw Twilight, and Rook sitting down having a bowl of oatmeal. Rook, seeing Ben enter, spoke up.
"Hey, Ben! Come on and try this oatmeal Spike made. It's good."
Ben took a seat as Spike gave him a bowl. Twilight spoke up, "We were just talking about how to find more traces of Morningstar in Equestria."
"Assuming he hasn't already drained many of the creatures that inhabit this land." Ben said.
"Don't count Micheal out, just yet," Rook warned her, "Knowing him, he's found some way to take cover and survive."
"And with his powers you can already imagine the kind of harm he can bring to this worlds inhabitants." Ben added.
"Well, the princess still has guards all over Equestria trying to find a hint of what you described him as." Twilight assured him.
"Perhaps we should also do a routine check of this land?" Rook suggested.
"Go around all of Equestria? XLR8 would be up for that," Ben said.
"It would be wise to further get the layout of this land," Rook admitted.
"And my friends and I can help you with that," Twilight offered.
"We really appreciate what you're doing for me and Rook, Twilight," Ben smiled.
"What're friends for after all?" she asked.
"Friends?" Rook asked.
"Yeah, I'd like to think of you guys as my friends, as does Spike and the rest of the girls." Twilight explained.
"Yeah. Pinkie would normally say you can never have too many friends." Spike said.
Pinkie suddenly popped up between Ben and Rook, "You took the words right out of my mouth, Spike."
"Pinkie, when did you get here?" Ben asked.
"Just now." she grinned.
"I didn't even see you enter the castle." Rook said in shock.
"That's Pinkie for you." Twilight said.
"So you're all planning to tour Equestria? This is great, I gotta tell the girls. I'm sure they'll want to come along!" Pinkie said, as zipped off.
"And there she goes." Spike said.
"You really have strange friends, Twilight." Ben said.
"They all have their unique quirks," She nodded, "But that's what makes them special." she smiled.
Meanwhile, inside Sombra's dark crystal castle: the Shadow ponies, Sombra, Micheal, and his newly assembled gang were at their meeting table.
Trixie spoke up, "So what do we do first, Micheal?"
"First we need to find the location of Ben 10." he explained.
"And how long will that take?" Gilda asked in boredom.
"Patience," Sombra ordered, "My Shadow minions are already scouring all of Equestria to find him."
"How hard could finding him be if he is anything like Micheal?" Albedo asked the group.
"Do not underestimate Tennyson," Micheal spoke up, "Finding him is just as difficult as finding a needle in a haystack."
"When ya put it that way we could be here for days." Lightning Dust grumbled.
"I don't care how long it takes. I will find Ben and make him pay!' Micheal slammed his fists on the table, startling Sixsix and Sevenseven.
Suddenly a Shadow pony entered and spoke, "You're excellency. I bring news."
"Speak." Sombra permitted him.
"I've located the one Micheal called Ben 10."
Micheal did a double take and asked, "You have?"
"Yes, but I'm afraid there is a problem." the Shadow pony added.
"How so?" Micheal crossed his arms.
"He's not alone." the shadow pony continued.
"What do you mean not alone?" Kraab asked, annoyed by the vagueness.
"They have others with them. And not just others. The same ponies who stopped you from reclaiming the Crystal Empire." the Shadow pony finished.
Sombra's eyes widened and a frown formed on his face, "What?"
Micheal eyed him, "Judging by your reaction, I assume your minion just spoke of the enemies you told me about?"
Sombra answered, "Yes. Twilight Sparkle and those five friends of hers. If it weren't for her finding the Crystal heart and giving it to the Crystal ponies I would have been ruler of the empire once again."
Micheal smirked, "Well, now's your chance to get even."
Sombra returned the smirk, until Gilda stood up, "Finally we can get in on some action."
"Not so fast," Sombra interrupted her, "The last thing we want is to suddenly give them the hint that we're all in an alliance."
"Sombra is right," Micheal nodded, "For now we will strike at them in waves, starting with Sombra's Shadow ponies."
"Oh, damn," Trixie grumbled, as she sat back in her seat, with Gilda looking equally irritated.
Sombra stood up, "I'll take my army and do away with Ben 10."
"Be careful, Sombra. Underestimate your opponents and they'll bite you hard." Micheal warned him.
"Duly noted." he answered, before he and his army vanished.
Back with the heroes, they were walking though a forest, Rainbow Dash was flying above the trees,
"So you don't always get the alien you want to turn into?" Twilight asked,
"Yeah, it's so annoying" Ben answered. The group continued to walk forward.
Suddenly, from out of nowhere came a bolt of what look like black smoke, which quickly turned itself into a small army of black coloured ponies.
"What are those things?" Ben asked,
"They must be Shadow ponies" Twilight replied,
"Looks like it's hero time" Ben said, he turned the dial on the Omnitrix and slapped it down, he charged at the attacking shadow ponies.
One of the Shadow ponies fired a magical blast which hit Ben and sent him flying a few feet,
"Oh, my!" Fluttershy exclaimed in fear that Ben might be hurt,
"He'll be OK" Rook reassured her,
Twilight, her friends and Rook charged at their attackers.
Ben, meanwhile had recovered from the hit he took, he got up on his feet then he saw who he had transformed into the water shooting alien, Water Hazard.
"Oh, Water Hazard" he groaned, "Why can't I ever get Humungosaur?"
Rook was dodging some incoming Shadow ponies before two of them grabbed him by the arms, "Let go!" he ordered as he clonked their heads together.
As Rook was doing his best to keep his friends safe, Water Hazard spoke up, "Rook! Lets give these creeps the cold shoulder!"
Rook abiding by his request began driving the attacking Shadow ponies into a tight group,
Water Hazard then slapped the Omnitrix symbol on his chest and in a flash he transformed into the ice breath alien Articguana,
"Not what I was going for... but I can work with this" Articguana said, a bit annoyed it wasn't the alien he had in mind, but it had the right ability for the job.
"Ben, I can't hold them like this much longer" Rook shouted,
"Right" Articguana replied, he turned to face the group of Shadow ponies he took a deep breath and a beam of ice shot out of Articguana's mouth. It hit the group of shadow ponies freezing them solid.
Articguana transformed back into Ben, he and Rook rejoined Twilight and her friends,
"Why do you think those Shadow things attacked us?" Ben asked,
"There's only one pony who can command creatures like those" Twilight replied, "King Sombra"
"B-b-b but I thought Sombra was banished after you found the Crystal Heart, Twilight" Fluttershy said, almost speechless,
"We'd better get to the Crystal Empire, and fast" Applejack said,
As the ponies, Ben and Rook turned to go they heard a sound that sounded like breaking ice. One of the Shadow ponies had manged to melt himself free from the ice,
"I must destroy you all" he snarled, "my king commands it",
Before Ben or Rook or the ponies could react, the Shadow pony fired a magical bolt at Twilight. Ben, thinking fast, threw himself in front of Twilight, the blast ended up hitting his Omnitrix, "Danger, stabilizer damaged" it said,
The Shadow pony quickly vanished. Ben looked down at the Omnitrix which had started to buzz with what looked like green lighting, "Not Good" He said,
Then everything happened at once: the green lighting shot from the Omnitrix striking the ponies and Spike knocking all of them out cold.
Twilight was the first to wake up. "What happened?" she groaned, bringing a hoof to scratch her neck. To her surprise it felt as if it wasn't there. Then with a shock she saw what had happened to her: her head was now floating in mid-air, her body had stripes of black on it and out of her shoulders now sprouted two spikes; she still had her horn but her wings had completely gone. Twilight screamed, out of shock and fright.
The sound of Twilight's scream woke Rainbow Dash up, "Arr, my head" she said, when Twilight saw what Rainbow Dash had became she nearly screamed again. Rainbow Dash had become something completely different than what Twilight had become. Her head was covered by a bullet shaped helmet, her rainbow coloured mane was still visible poking out from the helmet, she had black wheels attached to her hooves; she still had her wings but they were covered up. "What are you looking at, Twilight?" asked Rainbow Dash, noticing Twilight staring at her.
Rainbow Dash then noticed what had happen to Twilight, "Wha, what happened to you, Twilight!?" Rainbow Dash asked, staring at the pony creature standing in front of her,
"More importantly, what's happened to both of us?!" Twilight blurted,
Rainbow Dash looked at her hooves and noticed the black wheels attached to them, "OK, not the weirdest thing that's ever happened to me" she said. Unlike Twilight, she was completely calm, almost.
The two then turned to where Rarity, Fluttershy, Applejack, Pinkie pie and Spike lay and they were more shocked at what had happened to them.
Applejack looked a little bit different to the others. These differences were: an extra pair of front legs, an extra pair of eyes and she had grown more muscular. 
Fluttershy looked a lot different then Applejack, she had became what looked like a fusion of a Pegasus and a wolf. Her yellow coat and pink mane had became slightly darker.
Pinkie pie's look was even more stranger then Applejack's and Fluttershy's, her body was completely made of pink coloured slime-like liquid which seem to be supported by a UFO-like device hovering over her head.
Spike had became what looked like a fusion of a dragon and a fish person, he had webbed feet, webbed figures and a pair of oversized jaws.
After looking at what Twilight and Rainbow had become, Applejack and the others then turned to look at Rarity. They all gasped and stared. For what had happened to Rarity was far more terrible then what had happened to the others.
Rarity looked like her normal self, the only three differences were the nozzles all over her body, the window in her stomach where swirling gas could be seen and her usual white coat now turned a sickly purple colour.
"What's wrong?!" asked Rarity, not knowing what had happen to her, "is there something on my face?",
"No, it's nothing" replied Fluttershy, trying to stop staring at Rarity,
"It's not that bad" added Applejack,
"It's... wired" Finished Spike.
Shortly after saying then Spike began to started wheezing and coughing,
"What's wrong Spike?" asked Applejack, she, Fluttershy and Rarity rushed over to the fish-dragon.
"Can't....breath....need....water" Spike wheezed. Because Spike now had DNA from a fish he couldn't survive out of water for long,
"What did your Omnitrix do to us?!" Twilight asked Ben,
"I think this has happened before" Ben replied,
He quickly explained what had happened to him when a similar event with his Ulitmatrix had transferred its power into his friends, "So what your saying is that your Omnitrix's power got transferred into us" Twilight said, slowly trying to wrap her head around what Ben had told her.
"Can you change us back then, sugarcube?" asked Applejack,
"And....fast" Spike wheezed, practically dying of dehydration,
"OK, here goes nothing" Ben said. He twisted the dial on the Omnitrix a few times and in a flash of green, Twilight, the others and Spike changed back to their normal selves, the only thing that didn't changed was the fact that now there were Omnitrix symbols on everypony's chests.
"What now?" asked Rook,
"We have to head to the Crystal Empire, fast!" Twilight said, "my brother and Princess Cadance might be in danger",
"I'll bet Way Big could get us there" Ben said, he slapped the dial on the Omnitrix, but nothing happened,
"What's wrong with it?" Rainbow Dash asked,
"It's got to recharge" replied Ben,
"You've got to be kidding me? It has to recharge!?" Rainbow Dash repeated,
"Those transformations during the fight and the damage it took must have drained all its power" Rook realized,
"So I guess we'll be taking the train to the Crystal Empire then" Rarity suggested,
"It looks that way" Twilight replied, as she and the others all started walking back to Ponyville.