Back in Canterlot Castle
"Every minute brings you closer to becoming human again," Zs'Skayr, still inside Luna, smiled, as he fired magic blasts at Snare-oh, "then finally I will merge with you and become whole again."
"More than enough time to kick your ghost butt from here to Anur Phaetos and back," Snare-oh replied.
"You wit is just as annoying as all the other times we fought," Zs'Skayr growled.
Before Snare-oh react Zs'Skayr hit him with a huge blast of magic, Throwing him backwards and forcing him to turn back into Ben.
"Any last words, Tennyson?" Zs'Skayr asked.
"Two actually," Ben choked, "Breath. Mint."
"I will enjoy wiping your worthless existence from the face of creation," Zs'Skayr thundered.
But before he could act, Zs'Skayr was hit by a blast of magic, forcing him back.
Both Zs'Skayr and Ben turned to see Princess Twilight standing there.
"Leave him alone," Twilight said, slowly.
"So the real Princess of Friendship decides to show herself," Zs'Skayr smirked.
"Get out of that body," Twilight continued, "you don't need it."
"What do you expect to see if I do?" Zs'Skayr asked.
"The face of a mistake I made," Ben said.
"Very well," Zs'Skayr smiled, with that he phased out of Luna, who fell unconscious.
Ben slapped the omnitrix and transformed into Diamondhead "Time to end this." he said.
"Together." Twilight agreed.
"Fools," Zs'Skayr laughed, "when you're in the darkness of the night, I am at my full potential."
Energy surged around Zs'Skayr, tentacles sprang from his chest and spike sprang from his shoulders.
Diamondhead and Twilight charged at Zs'Skayr.
Back outside
Ultimate Waybig had successfully defeated Mad Waybig and now was helping the others fight the bad guys, now in the form of Cannonbolt.
"Hey Ben!" Vinyl cried, "You up to bat?" she had rounded up so of the evil Elements and dazed them with her wub blasts.
"You know it," Cannonbolt replied, he slapped the Ultimatrix symbol and transformed into Ultimate Cannonbolt.
After he had transformed Vinyl moved out of the way and Ultimate Cannonbolt rolled up into a spiky ball and charged at the rounded up villains.
"Strike!" he cried, as he unrolled.
"Surprise Tennyson!" called a voice.
Ultimate Cannonbolt turn to see Albedo, "You look different," Cannonbolt said, "did you get a hair cut?"
"Your just as annoying as all the others," Albedo growled, he slapped his omnitrix and transformed into Ultimate Echo Echo.
"I see you got you knock off Ultimatrix working again," Ultimate Cannonbolt said, as he changed back into UA Ben, "for like the third time?"
"Yes," Ultimate Echo Echo replied, "now I can get revenge on you."
"Same old song," UA Ben said, rolling his eyes he slapped Ultimatrix and transformed into Big Chill and then to Ultimate Big Chill.
"Just like old times Albedo," Ultimate Big Chill remarked, "you, me and fire so cold it burns."
"Oh, let's break it down!" Vinyl smiled.
Vinyl and Ultimate Big Chill engaged ultimate alien in battle.
Elsewhere in the battle.
Trixie face off against her doubleganger Magic Mare. 
"Wait a minute, your suppose to be me?" Trixie said, as she dodged Magic Mare's attacks while counter attacking, "I wouldn't go out in public looking like that."
Magic Mare just smiled maniacally and continued her attack.
Finally, Atomdrillo faced off against Maltruant.
"Once I destroy your past, you will cease to exist," Maltruant growled, as he fired time rays at the future hero.
"Same old, same old," Atomdrillo yawned, as he changed back to Ben 10,000, "its all the same with you villains."
In a flash, Ben 10,000 transformed into Atomic-x (a fusion of Alien x and Atomix)
Both Maltruant and Atomic-x changed at each other.
Back inside the castle
"Do you really think the two of you have a chance against me?!" Zs'Skayr laughed, he fired blasts of energy from his chest.
"I've beaten you before and I'll do it again," Diamondhead replied, firing diamond shards at Zs'Skayr and blocking his blasts.
"My power has grow ten fold since our last battle," Zs'Skayr smirked, "nothing came stop me, not even your omnitrix."
"As long as there is life, there is always hope," Diamondhead cried, he and Twilight fired on Zs'Skayr.
He turned invisible and attacks pasted through him, after which he blast Diamondhead with a powerful blast, sending him flying back.
"Tell me Twilight, hows your niece Flurry Heart?" Zs'Skayr asked, as he moved closer to Twilight, "with you and your out saving all Equestria she's likely to got lonely, how about I pay her a visit?"
"Don't you touch her!" Twilight thundered, she blasted Zs'Skayr with her magic, "stay away from her, you hear me you monster!"
She blasted Zs'Skayr again, he simply blocked it, "What about your friends in the human world, Twilight?" he asked, "should I visit them?"
Twilight growled and fired an almighty magic blast at Zs'Skayr, knocking him to the ground.
"Well done, Twilight" said a voice, Twilight turned to see Princess Luna, who had regained conscious.
"Luna," Twilight smiled, glad to see her up and about.
"Good to see you're alright," Diamondhead added, getting back to his feet.
"Now what to do with you," Twilight said, looking back to the defeated Zs'Skayr.
"No, its not over," Zs'Skayr replied, franticly "my interdimensional teleporter is powering up I can still rule, I can still conquer, I can still...."
Before he could finish Diamondhead changed back into Ben, smiling he slapped the omnitrix and transformed into Toepick.
"You and Luna might want to look away," Toepick said, turning to the two ponies, "this isn't going to be pretty."
Zs'Skayr charged at Toepick, the metal cage helmet on his head opened.
Zs'Skayr stopped in his tracks, "No please," he pleaded, his body turned white as he collapsed into a shivering, trembling mess on the floor.
With that Toepick transformed back into Ben, he turned to Twilight and Luna, "This bits yours," he smiled.
Luna nodded, she walked towards Zs'Skayr, "You are not welcome in my world ever," she said, her horn glowed and the moon moved away from the sun, allowing the sunlight to flood the the room.
Zs'Skayr screamed as the sunlight touched him, causing his whole body to burst into flames, by the end he burned into nothing.
Back outside.
The heroes had rounded all the evil version along with the last of Zs'Skayr's forces.
"Right that's all of them," Trixie said, "Now what?"
"I could use my magic to teleport them back to were they came from," Starlight suggested.
"Not to worry," UA Ben interjected, "I'll take care of that," he slapped the Ultimatrix and transformed into Clockwork.
"Here goes," Clockwork said, after turning the key on his head, he fired a blast from his chest at all the evil version, causing them to vanish.
"Where'd they go?" Rainbow Dash asked.
"What did you do?" Starlight added.
"Just sent all of them back to the timelines they came from," Clockwork replied, as he changed back into Ben.
"So its all over," Thorax sighed.
"Yes, my little ponies," Celestia agreed, "its all over."