One cloudy day on Mystic Island, Mr. Grandruler and Principal Celestia were woken up by a certain fairy type Eevee evolution whom was ticking their cheeks with her feelers. "Sylveon... stop." Celestia groaned, wanting a few more minutes of sleep, by the fairy type pokemon would not hear it and she started nuzzling their cheeks trying to wake them. But what woke them up in the end was..

"Mommy, Daddy wake up wake up!"

Their children, Castor and Leilani came into the room and playfully tapped their mother and father. The two of them sighed and eventually sat up. "Alright, you win." Celesto said.

"Yeah." the children cheered.

"Sylveon." Sylveon added.

The two rolled their eyes. When Sapphire introduced her pokemon friends to the children, they immediately took a shine to them so Sapphire and their mother and father made an arrangement. Sapphire let Sylveon, Umbreon and Espeon stay at the mansion while all the other pokemon would stay at her castle.

Umbreon took a liking to Luna and Luna like Umbreon too.

The two of them got ready for the day and entered the massive kitchen to find Vice Principal Luna finishing making breakfast. "Hello Sister, brother-in-law." she greeted.

"Morning sister." Celestia said.

"Morning Luna." Celesto added.

"Morning Auntie Luna." The children said cutely. Luna smiled and the family all sat down for some breakfast. Celestia got some pokemon food for the three Eevee Evolutions and they ate along side the family. When they were all done, the three of them headed out the door ready to start their day while the children would stay with their pokemon babysitter, Sylveon.

The three of them decided to see how the college students and their friends were doing. Though when they all entered the college, they found it ominously quiet. Usually, there were students just arriving, including the Starfleet gang and the girls. "Okay.... this is odd." Celesto said. "Usually the students are here by now."

Espeon and Umbreon walked ahead of them and opened one of the college dorm rooms. "Umbreon."

Luna came to her pokemon's side. "There's no on in this dorm room."

Celesto and Celestia looked in Sunset, Artie and the others dorm rooms. "There no one in here too." Celesto said.

"This doesn't make any sense." Celestia said.

Suddenly, the doors burst open and Sapphire, Cadence, Shining Armor, Marla, Bronc, Keto and Sapphire's pokemon came in. "Sapphire, Cadence, Shining Armor, Marla, Bronc Keto? What are you doing here?" Luna asked.

"We were looking for you three." Marla said.

"Why?" Celesto asked.

"Everyone on in Mystic Island has vanished." Sapphire exclaimed in worry.

"Vanished?!" The three exclaimed in shock.

"Yeah, your three are the only humans we've seen today. Even those pesky magical friends of yours are gone." Keto said. Celestia looked at her sister and husband with extreme worry. "This is not good." Celestia said.

"I know we have to find everyone." Luna said.

"But where do we even begin?" Celesto asked.

"Espeon!"

Everyone looked and saw Espeon holding a brown book in her mouth that had Sunset's marking on it. "Sunset's book. We can use this to get in touch with Commander Lightning Dawn. Maybe he knows what might have happened." Celestia said.

"Excellent." Sapphire took out a pencil and she began writing in Sunset's journal.

Sapphire stopped writing and immediately the book vibrated and glowed red. "That was fast." Marla said.

"Us?! Go to United Equestria?!" Celesto exclaimed.

"We've got no choice, Earthman." Marla said. "We have to find anything that can help find the others."

"Marla's right. Come on." Keto said.

"Wait, what about Castor and Leilani?" Luna reminded.

"Bring them too." Bronc said. Celestia and Celesto were not too keen on taking their children to another world, but they could not leave them hear with the posibility that they could vanish as well. "... Alright." Sapphire used her magic to teleport, Sylveon, Castor and Leilani to the school. "Hi Mommy, Hi Daddy. What's going on?" Leilani asked.

"Children, we're umm.. going on a little trip, okay." Celestia said.

"Alright." The children said. Everyone came before the College's statue. "Ready everyone?" Sapphire asked.

"Ready." Everyone said and the pokemon nodded. All together they all jumped into the portal and they appeared in United Equestria or more specifically, in the royal throne room. Lightning Dawn and their majesties were there to greet them. The Grandrulers' felt a little awkward seeing their pony counterparts.

"I received your message, Sapphire. Please tell us everything." Lightning said.

"There's not much too tell, we don't really know what happened. This morning, everyone except for us was just.. gone." Sapphire said.

"Was there anything that happened in the past few days that may have anything to do with the disappearances?" Queen Celestia asked.

"In the past few days... ummm, I don't think so." Human Celestia said.

"Hmm.. if nothing has happened in the last few days then this disappearance was not natural. It sounds like Equestrian Magic is at work in your world." Grand Ruler said.

"But what kind of magic could make everyone but us vanish?" Marla asked. "And don't point your fingers at us!"

"Ww don't have a definite answer but the answer may be in the New Canterlot Library." Queen Celestia said.

Their majesties and Lightning Dawn led the group to the New Canterlot Library. They guided them to the far back of the library where the hallway was lit up with torches on either side. They opened the door and saw many shelves of books. Sapphire gasped at all the book, since she loved books.

"Oh my gosh, Oh my gosh, oh my gosh, so many books all unread. Ancient historical artifacts. I just... It thought.. I can't." She took a deep breath while the gang tried not to laugh. "Your sure you wanna look through all these books?" Celesta asked with a smirk. "Don't take this away from me?!" Sapphire exclaimed. She flew up to one shelf and grabbed a book in her magic. "Original weather warning from the Pre-Equestria Era! EEEEEEE!"

The gang looked at their majesties and Lightning Dawn and they shared a laugh at Sapphire's moment. Anyway, they looked through all the books. "Everyone, I think I found something!" Marla said, holding an ancient scroll. Everyone gathered around and Marla unraveled it. "The Vanishing Stone?" Human Celestia asked.

"Yeah, the scroll says it belonged to an evil wizard. With it she was invincible with the Vanishing stone she could make anyone vanish into thin air even whole town and cities." Marla explained.

"Town and cities... like Mystic Island." Celesto said.

"Clover the Clever knew that the stone had to destroyed so he chased after the wizard but every time he got close she would use the stone and put him in an entirely different area." Marla said.

"But then how did he catch her?" Keto asked.

"Clover remembered landmarks in the last area before he was teleported away and he returned to the spot and picked up her trail, like a trail of breadcrumbs." Marla said.

"So what happened on the other side of this scroll?" Human Celestia asked. Marla unrolled the scroll to revealed that it was torn!

"The rest of the scroll is torn. Clover must have hidden the Vanishing Stone to prevent anyone from finding it again." Marla said.

"Wait a minute... guys what if the Vanishing Stone somehow ended up in your world?" Lightning suggested.

"And someone used to to make everyone but us disappear." Sapphire said.

"But who?!" They both said in unison.

"Darn another dead end." Keto grumbled.

"Not quite. Now you all know what you are looking for." Grand Ruler said.

"Yes, but we still don't know how to find everyone." Sapphire said. Suddenly a purple light appeared behind them and they all saw a sparkling Twilight. "What the-? Whose that?" Keto exclaimed.

"That would be the Tree of Harmony in Twilight form." Lightning said. The Tree of Harmony nodded, "I am here to lend my assistance." it said.

"How?" Sapphire asked.

"Sapphire, your Elements of Harmony can locate your missing friends." The Tree of Harmony said.

"They can?! How?!" Sapphire asked.

"All you have to do is concentrate on all the memories you've had with your friends and the Element will respond to your heart and create a path that shall lead you to them in the end."

Sapphire was in awe. "Well what have we got to lose."

Everyone nodded. "Good luck, everyone." Grand Ruler said.

Everyone bowed to their majesties. "I'll go with them too, your majesties." Lightning said. Their majesties agreed and the whole gang went back through the portal and were materialized in front of Canterlot College. "Now where did you keep her Elements, sir?" Lightning asked Celesto.

"In the mansion, this way." Celesto led everyone to the mansion and upstairs to his room. Behind the dresser was a small safe. It unlocked it revealing all six of Sapphire's Elements of Harmony. Sapphire placed them on her wrists and head. "Okay... here goes nothing." She began concentrating, thinking back to all the good times she's had with her friends.

When they helped her overcome her past and helped her make a new start. How they guided her and cared for her, like she was one of their own. How she helped them in many battles and protected them and how they protected her. As she was her Elements shimmered brightly and all at once they shot out a rainbow beam on the floor that lead out far across the sea. Marla looked out the window. "Hey it worked!" she exclaimed happily. Sapphire opened her eyes and her Elements stopped shimmering. She looked at the path that was made by the Elements.

"Looks like we found our lead." Sapphire said.

"Right, we head out at once." Celesto said. Everyone nodded and they all headed out of the mansion and ran towards the beach. "How are we gonna follow the trail across the ocean?" Keto asked.

"I got this... Megalodon I choose you!" Sapphire called. And before anyone knew it the large shark burst from the depths of the ocean with a mighty roar and swarm towards the beach. It stopped in the shallows. "Hi, boy. We need you to follow this path across the ocean to find our friends and everyone." Sapphire said to him. Megalodon roared in agreement and opened it's mouth.

Sapphire took out many pokeballs. "Alright everyone, return." The pokemon were turned into red energy and went into the pokeballs. "All aboard, people and monsters." Sapphire said. They all piled into the Zord and Sapphire sat at the cockpit along with the others. "Alright boy, let's go."

Megalodon Zord roared and swarm back into the ocean and followed the sparkling rainbow path. "I hope they all are alright." Cadence said.

"Don't worry, Cadence we'll find them." Celesto reassured.

"Yeah those pests-" Bronc started but was cut off. "Ahem." Sapphire said with a raised eyebrow.

"I mean, teens are harder to get rid of."

"But still." Cadence added.

Sapphire turned to Cadence, "We'll find them, Cadence, I promise." Sapphire said with a smile. Everyone gave a small smile. "So what do we do about the Vanishing Stone?" Marla brought up.

"Hopefully where and who ever this path leads us too, we'll find the Vanishing stone as well." Celesto said. Megalodon kept swimming until it came to a remote island with what looked to be a facility on it. "An island with a facility? Why would your Element lead us here?" Keto asked.

"I don't know but if my elements says they're there than they are." Sapphire said. Megalodon came up on land and everyone exited the Zord. "Thanks boy." Megalodon blinked and retreated back into the water. Everyone looked at the facility and Sapphire felt something.... she felt like she knew this place... but she didn't know how.

"Sapphire, are you okay?" Celestia asked.

"Y-Yeah, I just... feel like I know this place... for some reason." Sapphire said. The sparkling path crawled along the sand and towards the facility. "Well... let's follow the path." Marla said. Everyone followed the path straight to the facility and saw the sparkling path going underneath the door. Celestia opened the door, which was surprisingly opened. "Odd... why would someone leave the door open?" she asked.

Nobody had a clue and they slowly walked down the hallway. Looking around they saw glass cages with animals and fossils in all of them. From tigers to monkeys from birds to lizards and even dinosaur fossils. "Oh my, who is keeping all of these animals?" Celesto asked.

"Something tells me I don't want to know." Shining Armor said. They approached one cage that was empty for some reason. Marla saw a clipboard with a paper on it. "Hmm... Experiment 201... Hybrid Human?!"

"What?" Celesto looked at the paper.

"The rest is too smudged. I can't read the rest of it." Celesto said. Sapphire had wandered ahead and she entered a large chamber that was dimly lit. "Hello?" she called out. "Anyone... here."

"Well, well, well." a voice said.

Sapphire gasped and the others immediately came over to see a brown skinned man with short, black hair wearing a lab coat. Along with four other man. The second man was tan with short, brown hair and he had glasses. The third one was light skinned with dark brown hair. They were all wearing lab coats too.

Sapphire stared at all of them for a good long moment before she gasped and her face turned angry. "You four?!" she growled.

"Yes.. I was wondering how long it would be before you returned." the brown skinned man said.

"Sapphire, you know them?" Shining Armor inquired.

"Know them? These four... are my creators."

Everyone gasped in utter shock and horror.

"They're your creators?!" Celestia exclaimed.

"They were the ones who treated you like dirt." Celesto added.

"Come now, we didn't treat Experiment 201 like dirt." the same man said.

"Save it, David! You, Brad, Lucas and Leo all abused me when I was here!" Sapphire exclaimed.

"Oh now, now now, we didn't do that on purpose." David said with a smirk.

"Well from what Sapphire had told us, you most certainly did." Celestia agreed with an upset expression.

"And she told us there was only one of you who actually cared about her." Shining Armor said. "And she helped her escape from this horrible place."

David growled. "I knew Lucy had something to do with your escape Experiment 201."

"The name is Sapphire... Princess Sapphire to you!" Sapphire hissed. "Now let's get down to business.... what did you do with my friends and everyone from Mystic Island?"

"Oh... them..." Lucas clapped his hands and the entire chamber lit up. Everyone looked at gasped in horror. Everyone from Mystic Island was in cages like Sapphire was. They all cried in relief at the sight of them all. "Where are Sunset and my friends?!" Sapphire growled.

Brad laughed and snapped his fingers. More scientists came in with Sunset and the others all in one cage. "Sunset, everyone!" Sapphire cried. They all looked up and gasped in joy. "Sapphire, Mr. Grandruler, everyone." Lightning said.

"Get us out of here!" Rainbow said.

"How could you do this?" Cadence demanded.

"Oh getting them here was easy with this..." David pulled out an aquamarine stone with what anicent drawings of a eye on it. "The Vanishing Stone!" Marla exclaimed.

"With this young beauty I was able to bring everyone here so I could lure you back here so we can have ourselves a little deal...."

"What deal?" Bronc sneered.

"When Experiment 201 escaped I knew I had to create a new hybrid... but then I thought... why create one hybrid when I can make an entire army of hybrid humans. With their unbeatable powers by our side, we would rule the world." Brad gave him and small laser. "With this laser, I implanted the same DNA that Experiment 201 has and once I place it into all of these humans, they will be hybrids and will obey all of my commands!"

"You horrid mad man. No one here would every obey you!" Celesto exclaimed in anger.

"Oh but they will have no choice. I placed brainwaves within this laser so they are forced to obey my every command." David said. He eyes Sunset and the others. "Observe!" He pointed the laser at them. "NOOOOOO!" Sapphire raced in front of the cage, just as David fired the laser. It hit her right in the head and she began to scream in pain. "Sapphire!" Sunset cried.

"HAHAHAHA! Yes, obey my Experiment 201. You are my creation and you will become the next weapon for human kind!" David declared.

"You monster!" Lightning growled. "Sapphire will never be a weapon for you."

"Sapphire's not a weapon she's our best friend!" Fluttershy added.

"HAHAH! Such sentimental nonsense." Lucas smirked.

"It's not nonsense!" Dyno cried.

"Si, none of you had the heart to give her love and hope like we did." Myte added.

"Sapphire's stronger than you think she is." Rainbow added. "You'll never be able to control her."

"She may be a machine or weapon to you but to us and everyone on Mystic Island, she's our Princess and our friend!" Sunset called.

"YEAH!" All the civilians agreed.

"Pfft." Lucas scoffed. "Please, she just a weak experiment tool."

".... No... I'm.... not..." Sapphire said as she stared at the four scientists who gasped in shock. "Impossible, you should be fully under my control." David said.

"I'm.... more.... than... you... THINK!" In an instant, her Element blasted the four scientists, knocking them all to the floor and the laser bounced out of David's hand. "NO!"

Sapphire took out two pokemon balls. "Ampahros, Lucario, I choose you!" Ampharos and Lucario came out with proud cries. "Free the people." Sapphire ordered. Ampahros used discharged to sort circuit the locks and the cages opened. All the people leaped out of the cages and gathered near the Grandruler family and the minions. The four scientists growled as they stood up and they each took out on pokeball.

"Houndoom/Houndour, go!"

Two Houndoom and Two Houndour came out and growled at the two pokemon. Ampharos and Lucario got ready for battle when suddenly a blast came and hit the four pokemon. "What?" David cried. Out of the smoke appeared a light skinned women who was wearing glasses and she was wearing a lab coat with a kitten pin on it. By her side was a three-headed, draconic Pokémon with six thin, black wings that each end in two points on its back. It has a fuchsia-colored collar on its neck which surrounds its head. The main head is dark blue and has black eyes with fuchsia pupils. Its two hands are also black and each one harbors a head; these are similarly blue with black eyes with small fuchsia collars on the inside. Its abdomen has two fuchsia stripes and its feet appear atrophied, having no claws or defined soles and two or three small toes. Its tail also sports a fuchsia stripe and ends with a black tuft.

Sapphire gasped at the sight of her of and her eyes lit up. "Lucy!" she ran over and Lucy hugged her. "Sapphire, you're alright... thank goodness." The two of them were shedding some tears and all of Lucy's pokemon came over crying happily. "Sylveon, everyone." They all tackled her in a group hug. "Hehehehe, alright everyone. I see you found my surrogate daughter."

David growled, "Lucy, what are you doing?!" David growled. "I should have known you let Experiment 201 out of containment." Lucy's face turned sour, "Well excuse me if I helped her escape this prison full of people who saw her nothing more than a weapon rather than a human being and daughter!" she growled.

"Hydreigon." Hydreigon growled. Sunset and everyone else were in awe. Lucy really was the only one who cared for Sapphire. The four scientists growled. "Well if you want to take her you'll have to get past us." Leo threatened. Sapphire growled and stepped forward. "Gladly." Sapphire said.

"Honey, no!" Lucy cried.

"Don't worry, I'll be fine." Sapphire reassured giving her surrogate mother a smile. "Houndoom/Houndorur Attack!" the scientists cried. The four pokemon charged forth and Sapphire leaped into the air and changed into a puma. She slashed the Houndour, sending them crashing into their evolutions. Sapphire landed on the floor and blasted them all with a large sphere of magic, creating a large explosion.

"Oh my.." Lucy gasped.

The Houndour and Houndoom got up. "Use Flamethrower!" the boys cried and the pokemon launched four streams of fire at Sapphire but she used her magic and stopped the flames, absorbed them and blasted them back with twice the force.

BOOM!

The dark and fire type pokemon were sent flying and they crashed on the ground, knocked out. "WAAAHHH!" the boys cried. Sapphire changed back into her normal self. "You are not gonna control me or anyone else ever again!" Sapphire declared and she used her magic to blast the laser and broke into pieces. "NOOOOO!" David cried.

"Fluttershy, free the other animals, quickly!" Sapphire called.

"Right." Fluttershy said.

"We'll help too." Sunset said. Sunset and the others freed all the animals, "What do we do with the fossils?" Rainbow asked. Sapphire came over. "I can teleport them to Mystic Island." she used her magic to teleport the fossils off of the island. "Right, now let's move!"

Everyone began to ran towards the exit when the scientists blocked their path. "You're not going anywhere Experiment 201." Lucas growled.

"And why should we coward before you? There's four of you and hundreds of us." Luna claimed.

"Because we still have this!" David pressed a button and Sapphire was caught in a net and was dragged through a hatch in the ceiling. "Sapphire!" Sunset cried.

The four scientists laughed, "Bye Bye." and they disappeared down a hatch that opened beneath them. "No you don't!" Lucy jumped down the hatch. "Ms Lucy!" Sunset, the Starfleet gang, the girls and the Grandrulers leaped down the hatch too along with Ampharos, Lucario all the other pokemon and Hydreigon, leaving the minions and the civilians up top. "Come on people, let's get you outside." Marla said and the minions guided the people outside.

---

Meanwhile, Sapphire found herself tied by her arms and legs and hanging over a pool of lava. She struggled to get free but the scientists placed an anti-magic ring on her horn so she could not access her magic or her powers. David, Brad, Lucas and Leo appeared. "This is what happens to experiments whom disobey their creators!" David flipped the switch and Sapphire was beginning to be lowered into the lava. She gulped nervously. "Guys... where are you?"

Suddenly..

"Hydreigon, Dragon Rush!"

Hydreigon came and slashed the rope and caught Sapphire on his back. "Hydreigon!" she cried in joy.

"Hydregion."

"What?" David growled.

Hydreigon flew Sapphire over to her friends and pokemon, "Ah, you came to save our experiment, huh?" Leo taunted.

"No, we came to rescue our friend." Rainbow said.

"You four are not gonna hurt her anymore, you big bullies." Fluttershy said.

"We're Sapphire family now
So leave her alone and how!" Rhymey demanded.

The four scientists growled, knowing they've lost this round. "You'll pay for this Lucy and the rest of you too!" and the four man ran away. "Let's get them!" Rainbow cried ready to chase them but Lightning held her back. "Let them go, they can't do anything now."

"Lightning's right, let's just go home." Celesto said. Everyone agreed and soon they were on the beach once again with the minions and the civilians. "So... how are we gonna get back to Mystic Island?" Rainbow asked.

"I got this, Rainbow!" Sapphire said. She stood in front of everyone and she concentrated really hard and her horn and Element shined brightly with power and before everyone knew it they were back on Mystic Island. "We're back home!" Pinkie cried. "YEEEEEAAAAHHH!"

Everyone else cheered for joy as Sapphire panted heavily and she fell down on her behind. "You okay Sapphire?" Luna asked as she and her sister helped her up. "Yeah... just.... tired."

Lucy came up to her with tears in her eyes, "I'm so proud of you, Sapphire. I always knew you would become strong... I just didn't know it would be this strong." Sapphire shed tears as well and the two hugged each other.

"Lucy, we would love it if you could stay with us in our mansion." Celestia offered.

"Thank you very much, I'm sure David's probably gonna fire me anyway." Lucy said becoming a little sad.

"I'm sure I can find you another well paying job, Lucy." Celesto offered.

"Oh you're too kind, sir." Lucy said.

"Please Lucy, you're Sapphire's mother... it's just Celesto."

"Okay.. Celesto." Sapphire hugged her surrogate mother, happy that she was back in her life once more and now Lucy was beginning a new era in Mystic Island.

Next Chapter: Episode 4: A Second Sapphire? Estimated time remaining: 5 Hours, 31 Minutes