First and Last disclaimer for entire fic: I don't own Pokemon. And the Apprentice system belongs to a dead guy who I don't know.

A/N: I edited this chapter from the original I made, fixed some errors and added more depth into the characters. Personally, I think I went a little darker than what I originally had.

There are several AUs also, such as Jovi coming with Michael to stop Cipher.


A red haired boy, about ten or so, anxiously stood next to an elevator, waiting for something. He wore a yellow jacket and had a strange device around his left arm. Its chrome exterior fit perfectly well in the sci-fi room he was in. He waited patiently, hoping he wasn't too late. Just then he heard foot steps coming from behind him, as a younger girl, a Plusle and Minun perched both her shoulders, quickly dashed towards him. "Jovi, you're late!" The boy told the girl.

"Sorry Michael, Jovi will be faster next time." The girl, now identified as Jovi, told the older boy. Jovi, even though she was smarter than most people, always addressed herself in third person. She wore a white skirt. Around her arm was the same device on Michael's arm. "Jovi ready for Greevil!" She cried with both anxiety and joy, like Christmas had come early and Santa was having dinner with her. She was so innocent and sweet; it was a crime that she had to be involved with Cipher and the Shadow Pokemon. Yet she wasn't affected by the idea of stealing Pokemon to purify and set free.

Michael inhaled and exhaled, trying to focus his mind towards this particular battle. This battle was for all the marbles, the one final turning point in a war. He made his way towards the elevator, ready for what could be the biggest moment in his young life. The glass door opened and he walked into the tube. Jovi and her Pokemon sighed in unison, all three of them knowing that it wasn't the time for childish thoughts. As she stepped in, Michael pushed a button on the nearby elevator console and the elevator moved upwards.

Everything they did before has come down to in a single moment, the moment they remove Cipher from Orre. The moment to take their land from darkness. The moment they permanently liberate the Shadow Pokemon from the darkness. And most importantly, the moment to save the world.

When the elevator stopped, the two trainers found themselves in a large coliseum, without any people in the stands. Cold metal lined the entire room and sorrow whispered in the wind. The sorrow of the Shadow Pokemon that lingered long after their hearts were sealed filled the room.

A short, old man stood in front of them, as though he was waiting for this moment to come. On his face was a smile, not of joy and happiness, but of malicious intent. "So glad you could make it," he said in a sinister voice.

"Greevil, or should I say Mr. Verich?" cried Michael, "It ends now! Today, we shall defeat you and your XD001 I don't know what Pokemon it is, but it will surely fall!" Jovi took pride in the fact that Michael was the one saying this, most of the time he was a carefree and happy person. But when it came to Shadow Pokemon, Michael seemed as though he was replaced with a person who didn't understand giving up, and sometimes mercy. Jovi, of all people, should know, they were bother and sister after all.

Shadow Pokemon are Pokemon that have had their hearts sealed by twisted science. They were cold and heartless creatures that were infused with dark energies and hatred. They used attacks infused with dark energy. They were incapable of understanding mercy and honor. All they knew was to fight. They were fighting machines, nothing more, nothing less. Showing a Shadow Pokemon with kindness and friend ship then purifying it was the only way to save a Shadow Pokemon.

But Cipher was planning to create what was called an XD Shadow, a supposedly impossible to purify Shadow Pokemon. It was the plan for the ultimate killing machine, with little hope to defeat. Stopping the development of these Pokemon was the sole reason why Michael and Jovi set out to defeat Cipher.

Jovi snapped back to reality as she ordered Plusle and Minun into battle, while Michael released his Espeon and Flygon from their Pokeballs and sent him into battle.

"Normally four against one is an unfair fight," Greevil laughed, "but you will be fighting the soon to be Father figure of all Shadow Pokemon. Fight him if you dare! Come forth, XD001, Shadow Lugia." Greevil declared. The Coliseum around them seemed to open up, revealing a black winged creature coming towards them. A birds like silhouette entered the arena, striking a thunder clap of fear. Its wings and body were black from head to toe, except for the vicious red eyes and the white belly. "After this, your Pokemon shall become excellent Shadow Pokemon and will look up to XD001. Shadow Lugia, I command you to use Shadow Blast on them." The Shadow Pokemon didn't hesitate, not out of loyalty, but out of lack of free will, and fired a vacuum of darkness at Michael and Jovi's Pokemon.

"Jovi thinks this is bad," Jovi told her bother. "Plusle, Minun, Double Helping Hand on Espeon!" When ever Jovi does not talk in third person, she's serious. The two electric-types quickly had hold of Espeon and stared at the powerful vacuum attack.

"Espeon, Hyper Beam!" Michael ordered. An ethereal glow surrounded the fox, giving it an almost other world appearance. Espeon launched a beam of seer toward the vacuum and the attacks collided, causing sparks to fly.

Helping hand was and attack which helped support another attack. But the Hyper Beam barely held out against Shadow Lugia's Shadow Blast, even with two Helping Hands. Although the beam wasn't strong enough to bypass the Shadow Blast, Shadow Lugia distracted enough for a clean shot. "Now, Flygon take Shadow Lugia down with a Double-Edge!"

While the beam attacks were still firing, Flygon rammed into Shadow Lugia, causing it to cancel its Shadow Blast attack. Flygon quickly escaped, before the Double Helping hand/Hyperbeam combo cut its way towards Shadow Lugia. The attack caused heavy damage and knocking darkling into. "Jovi, now's our chance!" Michael used his left arm to charge up a Snag Ball, a Pokeball designed to capture trainer owned Pokemon. He threw the Snag Ball at Shadow Lugia, but it was blocked by a huge stone. "Huh?"

"Jovi sees more Pokemon." Jovi told her bother, noticing there way a Rhydon, Tauros, and Exeggutor standing before them. "Jovi thinks Battle is in Michael and Jovi's hands..."

"You will not snag my precious Shadow Lugia!" Greevil declared. The Shadow Pokemon acted as a blockade between the Snaggers and Shadow Lugia.

"Let's take care of these guys first Jovi." Michael told his sister, his Aura Reader going haywire. While Michael took out a few potions and Pokeballs, Jovi sprayed a few Potions on their injured Pokemon.

"Michael right, we snag Lugia last."

Thirty minutes later, Rydon was finally snagged, along with Exeggurtor and Tauros. The tough battle took its toll on Espeon, Flygon, Plusle, and Minun. Jovi and Michael were at the ends of their wits seeing their Pokemon suffer greatly in battle. The poor creatures were acting as self sacrifices to end the terror that is Cipher. Shadow Lugia was still knocked out, but Greevil slipped in a revive to make it conscious again.

When Shadow Lugia was revived, a program in its brain told it to leave the battle, an anti-theft action to prevent snagging. Shadow Lugia departed from the battle and flew towards the sea, heading for another place where Cipher existed. "We will meet again, boy!" Greevil said as a helicopter flew behind him. The old man climbed into the flying machine and disappeared along with Shadow Lugia.

Recalling their pokemon left Michael and Jovi alone, or so they thought. They didn't realize it, but they were being watched. A man with red hair and a blood, red cloak stood before them. "Well played, but your battle isn't over." He said.

"Ardos? We didn't come here to fight you." Michael told the man.

Jovi gave a gasp. "Michael and Jovi already beat you!"

"Nor will you have to again. I have no Shadow Pokemon, but I bring news," Ardos told them. "Grand Master Greevil has left to Kanto to create more Shadow Pokemon. From there, he and an allied organization, Team Rocket, shall a mass a great force. A force that I no longer have any intention of joining." The cloaked man then stepped back, planning to hide in the shadows of the coliseum.

"Why should Jovi or Michael listen to bad man?" Jovi told the former Cipher admin.

Ardos sighed. "Because, I want my father back..." he said as he was completely engulfed by the darkness. Michael and Jovi nodded and took another elevator out of headquarters. When the made their way down, they found the Robo-Kyogre and left Citidark Isle. But they didn't realize Ardos was still watching them as he said to himself. "And I know both of you do also..."


Jovi and Michael stood before their mother and Professor Krane, the heads of the Pokemon HQ of Orre. Their top concern was Shadow Pokemon and how to stop them. After hearing of the events that took place in Citidark Isle, their mother gave them a tight hug. They were relieved when they heard Cipher left Orre, but was shocked to know where Greevil was heading. If Cipher or Team Rocket gained more Shadow Pokemon, it could spell trouble.

"Well, I'm glad to see you two are alright." Krane told the children. "You two will have to track Greevil down, before he controls more Shadow Pokemon. I better activate more snag machines, we'll need all the Snaggers we can get." Krane walked away, returning to his lab work

Michael was relieved that they could rest for a bit, he and Jovi practically went cross-country through Orre, battling Cipher nonstop. But his primary concern was not about himself or Jovi, but rather their Pokemon. They were heavily battered and injured in the battle and the moment they returned to Pokemon HQ, they were admitted into the Emergency Room. "How are our Pokemon?"

"You may see them if you'ld like." Their mother, Lily, told them. Michael and Jovi spilt up and turned to their respective Pokemon. Michael to Espeon and Flygon; Jovi to Plusle and Minun.

"You both did good today, I'm glad we did at least drive Cipher out of Orre." Michael told his Pokemon.

Espeon told Michael with his Psychic powers. "WE failed, Greevil got away!"

"It's our fault there will be more Shadow Pokemon..." Flygon said to his trainer, using the aid of Espeon's mental abilities.

"Well, then we're just going to have to do better this time." Michael told his Pokemon. "If we worry about it, yet do nothing, we will fail. But if we work hard enough, we will win and Cipher will be another name in the dust. Tomorrow, we sail to Kanto and make sure Cipher loses this time." Both Pokemon gave a silent smile to their trainer, both knowing he was right.


Max was excited about today. Today was his chance to finally have a Pokemon. He cheered as he leapt out of a guest bed in the Ketchum home. Normally Max would have received his license from Professor Birch, but he wasn't in Hoenn at the moment. Normally something like this would have annoyed the boy to no end. But then Max realized that none other than Professor Samuel Oak would present him with a Pokemon. He craved such an honor such as this the moment he heard the word "Pokemon".

Although he was too young to be a full-fledged trainer, he was old enough to be an apprentice. Apprentice trainers were a recently added concept that allowed kids a year from receiving a full license to start training Pokemon. An apprentice would have to stay and learn with his/her master and both must have a good amount of responsibility. An apprentice could not participate in Gym battles also, but can still capture some wild Pokemon. All of these conditions were acceptable to Max, considering he was still going to get a Pokemon and the word "trainer" appealed to him. Then there was his master to be, Ash Ketchum.

After the events that took place yesterday, Ash agreed to teach Max how to train Pokemon. Even though Max knew a lot about Pokemon, he didn't have much experience to use such knowledge. He was still confused to learn that a lot of the stuff he studied was able to be proved wrong.

Max slowly made his way to the ground floor, noting that his traveling companions were temporarily grounded, due to a supposedly missing Gym leader. Good news was that the Elite Four, the toughest trainers in a country, have sent one of their own to fill the missing place, so things can get back to normal (if there was ever a normal in their world).

Brock, the former Gym Leader of Pewter City, was a tan skinned and squinty eyed fellow with a desire to be one of the best breeders in history. He had a tendency to ask every cute girl out on a date and get rejected in a matter of five minutes(sometimes even seconds). Being a used to rock- and steel-types, Brock's Pokemon were usually defenders.

May, Max's sister, was busy thinking of new ways to train her Pokemon in contests and some fighting skills. Her Pokemon were Combusken, Munchlax, and Bulbasaur, which apparently had taken a liking to Ash's. Her battle and contest style was based on images and graceful movements. Although she was sometimes a bit crazy, she tended to be nice.

Misty, the once Gym Leader of Cerulean City, had decided once again to travel with Ash. Apparently, Brock's mother, Lola, who had once tried to make Pewter Gym into a water arena, decided to take over for a while. It could be said she loved water Pokemon with a fiery passion, if those the words weren't contradictory to each other. She had a tendency to hit who ever made her angry.

The Go-Getters weren't Pokemon trainers, rather they were Pokemon. They came from an island some miles south of Pallet, which was completely inhabited by Pokemon. Because this island was plagued by natural disasters, the inhabitants formed organized search parties called Pokemon Rescue Teams. Of these teams, Team Go-Getters was one of the oddest.

Maganuim, team leader, was related to Ash's Bayleef. She, unlike most others grass-types, who were usually passive and submissive, often took charge of the team. Back on the island, she leader her team through various places, including lava and deserts, and if the need arose, organized multi-team missions.

Charmeleon was easily the tamest, yet the most vicious, the most easily scared, yet bravest charmeleon in existence. Most of the time, he acts tame and plasters a smile on his face (plain unusual on a charmeleon if you ask me). Other times, he bursts into a rage that could scare the charzard of Team A.C.T. He was scared of some humans and had a paraniod fear some human would take him away from his friends. But if his friends, who included some humans, were in danger, he forgot the meaning of the word "fear". All of these behaviors were things a charmander would do which make it seem his brain refused to grow up.

Wartortle wasn't exactly your normal pokemon either, he was once a human. One day he woke up as and squirtle joined team Go-Getters as the medic. He helps his team mates by storing and managing all of the items he keeps.

Finally, Ash Ketchum, one-day owner of they house they were lodged in, soon to be Max's Master, and big dreamer, was still rubbing the eyes from his sleep. He had a miniature army of Pokemon at his disposal and knew their skills and abilities very well. His main Pokemon, Pikachu, usually was somewhere on his shoulders. Ash and Pikachu's encounters were with numerous people, most of whom were successful in their fields of work.

Max looked at his friends, all of whom were Pokemon trainers (or Pokemon in some cases) in someway, soon he would be one aswell. Max soon stepped closer to a nearby clock and gave a gasp. He quickly ran out the door, forgetting he was still wearing pajamas. On the clock it read 10:51

"De ja vu, huh, Pikachu?" Ash told his starter.

Pikachu giggled like a child as he told his trainer, "Just like you...He really would make a good apprentice, he even got late on the same time. I wonder what Pokemon he'll get..."

"I believe it wouldn't be one of the starters. Knowing Professor Oak, I think he already got a special Pokemon for him. We should be moving out soon as he gets it/he/she..."

At this, Team Go-Getters decided to make an exit for a while. "We'll get ready." Wartortle told the humans.

Max was scared. Not only he was going to get a Pokemon, he was going to receive it from Professor Oak. He took deep breaths and slowly made his way into the laboratory. He was soon standing face to face with Professor Oak and what looked to be a table holding three Pokeballs.

"Ah, Max so good of you to come..."Samuel Oak told the boy."I would tell you to choose a Pokemon, but well see for yourself." He directed Max to the table and he began opening the Pokeballs, to find them empty. Max started to seem like he had lost all hope, but Oak couldn't let the boy down that easily. He always kept a few extra Pokemon especially for kids who wake up late. "Wait just a second." Professor Oak pushed a button on his computer and a fourth Pokeball appeared on the table. Max slowly walked up to the table once more and grabbed the Pokeball. "I always carry a few extras, just incase."

Max gleefully opened the ball releasing a strange creature with a blue, bell shaped body and a single red eye. "Beldum..." it said.

"Wow a Beldum!" Max said awestricken. The Pokemon Max was staring at was deemed highly intelligent when evolved. And if there was anything Max valued, it was knowledge.

An hour later, Max and Beldum came returned to Ash's house. The pair rang the door bell, which Ash, being one of the people who lived in the house, answered. Both Ash and Pikachu were just weirded out when they saw Max and his new Pokemon, beaten and bruised. "Uh what happened?" Ash asked.

"Uh Beldum and I tried battling one of the nearby Spearow and then a huge flock came by and attacked. Then Beldum came using Take-Down all over the place. We kind of broke a bike, good thing the owner wasn't there..."Max said with worry. Ash and Pikachu just seemed startled that the boy had a first day almost exactly like that of their own.

Misty, while over hearing the conversation between the now master and student, slapped herself. She forgot to take her bike with her into Pallet Town, now it's broken, again. Was the world out to get her and her bike?