Disclaimer: I do not own Pokemon if I did Ash wouldn't be such a Joke.

A/N: Hey readers I am back, and ready to continue this story after a long break. Forgive me but real life issue came up that kept me away from writing Fanfiction. I am still much busier then I was before, but I will try to get an update at least every month from now on. For all those who have stuck with me, I thank you.

Tree Of beginning

Eberus avoided the incoming attack. Team Rocket's site looked like a bomb had hit it. From nowhere three Legendary Pokemon had appeared and interrupted their mission.

"Lucario use Focus Blast!"

Eberus' Lucario formed an orb of energy between its paws and unleashed it towards the group of Legendaries. One of the legendaries was a solid block of ice, with two large Icicles for arms and two triangles pointed feet. On the front of the body, small lights were blinking in a pattern. This was Regi Ice.

Launching huge boulders from another area was a large solid rock type Pokemon. Its body was a huge boulder, and its arms were made up of small rocks. Its legs were also formed by small boulders. Like Regice it too had several lights all blinking. This was Regirock

The last Pokemon had a large smooth dome-like body. It had long metal arms and metal legs. Again it too had blinking lights on its face. This was Registeel Flash cannon after Flash cannon was fired around the Rocket site. Several transport ships were now on fire.

Eberus heard the screams of the various Team Rocket Grunts, normally wild Pokemon were not this violent, and they wouldn't kill intentionally, but Eberus could sense their appearance wasn't a coincidence. These Pokemon were most likely Guardian of the Tree of Beginning and now it was under attack, they had awoken to protect it.

Eberus growled before he began to form large orbs of black aura in his hands. He aimed it towards the Legendaries along with his Lucario. He was just able to jump to avoid the stone edge that Regirock had unleashed across the terrain. Eberus noticed most of the grunts were fleeing to the woods only Domino and a few others were fighting back with their Pokemon.

"Cowards! Get back here and fight! Enough of this" Eberus visor lit up and he slammed his glowing black hands into the earth. Causing the ground to shake, suddenly the earth erupted in several places near the three Legendaries. Geysers of Dark Aura were surrounding them.

Far away from the battle, three small Pokemon looked on, as their parents tried to defend against the Aura guardians attack. They had been told by their parents should anything happen, they needed to seek out a trainer called Ash Ketchum, who would protect them, and train them.

The small Regice watched as his mum fell, he wanted to help but the small Registeel stopped him. The eyes on its face were blinking rapidly, and bleeping sounds could be heard.

"Regiice we can't interfere, you heard our parents"

The small Regice wasn't having any of it though and was now being held back by Registeel and the small Regirock.

"Come on Regice we need to find this trainer Ash, we can't save our parents on our own, that aura user is too strong."

"But Mum, she will be captured." Regice was the youngest of all the small Regi's

Registeel was the oldest and decided he needed to take charge.

"Come we have to get out of here. Dad said this trainer called Ash is on his way to the tree, so all we need to do is wait in the rocky terrain that separates the tree from the Kingdom. We are bound to bump into him."

Regice and Regirock reluctantly followed Registeel away from their parents who had all now fallen to the aura user and were being shoved into large cages.

Meanwhile, Ash and the girls were following Lucario who was leading them towards the tree of beginning. They had been traveling for a few hours. Normally they would fly but Ash wanted to take Team Rocket by surprise. Sabrina was holding the small Mew in her arms. They would take it back to the tree where hopefully it would fully recover. They were now nearing the rocky terrain that according to Lucario separated the tree of beginning from the main Kingdom.

"Hey Lucario could we stop for lunch?" Ash was feeling a little hungry the castle kitchen had provided them with a packed lunch for their journey."

Lucario turned his head towards his teachers descendent and nodded. Soon everyone had taken a seat, and food was being handed out. Ash and the girls were feeding all their Pokemon, and Lucario was amazed at how many Legendary Pokemon Ash had with him. He then noticed Ash handed him a bowl of small cubes with dusted color flakes.

"That's Pokemon food, that type is specially designed for fighting types, we have also dusted some berries over it which are also good for Pokemon."

Lucario took a bite of the small cube. His eyes widened in surprise, at first sight, the cubes didn't look that appetizing but now tasting them he found them to be quite delicious. Lucario noticed Ash took a seat next him. Lucario had been thinking about something, Ash wasn't the only person he could sense Aura from. It seemed Cynthia also had Aura, but how was this possible? Sir Aaron had told him only males could be aura users, so why was he sensing Aura from Cynthia.

"Ash do you mind me asking you a question?"

Ash was surprised by the request, however, he nodded. "Go ahead."

Lucario didn't want to come off as rude but he wanted to know. "How is it that one of your mates can use aura? Sir Aaron told me the only male humans can control aura."

This surprised Ash, he had no idea that aura users were males, so how could Cynthia use aura? Ash decided it was most likely a one-off, due to Lord Arceus' design.

"To be honest Lucario, I'm not sure myself, I can only assume it has something to do with Lord Arceus. He has been watching over us quite a lot and according to Sabrina he has a plan in motion, but I don't know what that is. Anyway, tell me what it was like to live in your time. You know swords, knights, all that middle-age stuff. "

Lucario frowned.

"The time you call the middle-ages, were not as glamorous as you make it out to be. It was a time of hardship and War. This Kingdom was in the middle of a growing struggle and was trapped between two other nations. Our Kingdom always ended up being the battleground. And the people of our kingdom suffered. However, the final battle was the biggest, and would have torn the kingdom apart, had Sir Aaron not sacrificed himself and used the tree powers, to help the Pokemon and people fighting, learn that war wasn't the answer."

Ash dropped his head. "Sir Aaron sounds like a great man. I've only read part of his journal but that it is nothing from hearing a first eye account of the man, and my ancestor. I just hope I can live up to his reputation,"

Lucario turned to Ash.

"When I first meet Sir Aaron, I wasn't trusting of humans. I watched him each morning from the shadows as he trained in the forest near my home. I became fascinated by his odd power. I watched him each day until one day Sir Aaron called out to me. It seems he had known that I had been watching him all this time. I wanted to retreat back to the woods, after all, you hear such horror stories about humans, and how some of them treated their Pokemon. I had also witnessed first hand when Pokemon I called my friends were captured and taken from their home. But something was different about Sir Aaron, I could sense no hostile intent towards me and so decided to show myself. He began to show me what he was doing and I found myself wanting to learn more. Over the coming months, it came apparent that I had the same gift for the aura, and so Sir Aaron decided to take me as his apprentice. I moved to the castle and became his pupil. He taught me all I know."

Ash leaned back against the rocks. "I can only do a few things, however when I get angry or upset my power sometimes goes out of control. I have been working and meditating to control it, but each day I feel that bit more powerful and worry that one day I will let it get the better of me. This aura user we will be facing, he uses black aura and has a black Lucario with red eyes. He's super strong. Far stronger then I am. In fact, the first time we met I had to retreat because he was so powerful. He wanted my two mates for himself. I couldn't allow that so my good friend Mewtwo teleported us away. However, I am worried that this time when I face him there will be no escape."

Lucario frowned. "I've only heard of Black aura, Sir Aaron told me it was Aura energy that had been tainted and it turns black when its user decides to miss use it. The taint is then passed on to the users Pokemon. That is why he has a black Lucario."

Meanwhile, over the otherside, Cynthia and Sabrina were discussing something important. It would soon be Ash's birthday, and they wanted to do something special as he would turning the big 16. The problem was they were traveling so it was no good planning a party or something.

"What about something a little personal, you know one of us, or maybe both of us."

Sabrina shook her head. "No, I don't turn sixteen for a month and you three months. We agreed that we wouldn't go any further then we have until we were all at least sixteen, but that doesn't mean we can't do things we normally do with Ash."

Cynthia groaned. "Well, what if we get the Pokemon League involved. I mean Ash loves to battle, maybe we can arrange for a few Elite four members for him to battle."

Sabrina thought the idea of Ash battling several Elite four was a good idea, but who. Ash had already beaten Loreli, Karen, Will, Agatha, Lance was out of the question, who was left. Sabrina pulled out her Pokegear and dialed the Pokemon League. However, before she could get an answer she and Sabrina was surprised by the sound of bleeping and looked up to the top of the cliffs where three strange Pokemon were looking down at them.

"Hey, Ash we have company."

Ash looked up to where Sabrina was pointing. Three Pokemon were now making their way down the side of the rocky terrain. He grabbed his Pokedex and pointed it towards the three Pokemon. Regice, Registeel and Regirock. Legendary Pokemon, but what were they doing here, and why were they coming towards him.

Pikachu jumped off Ash's shoulder and took up position in front of Ash, Lucario, however, looked surprised.

"Don't attack those are the guardians, they protect the tree of the beginning, however, they look smaller than I remember. In fact, they normally don't come out this far."

Ash was getting the feeling of de-ja-vu, three baby legendaries, this couldn't be good."

Meanwhile at the Tree of beginning

With the three Legendaries caged and on their way to Team Rocket HQ, Eberus had time to do a little exploring. He had sensed a change in the rock formation after he had driven Mew out. As his hand moved over each crystal a rush of power flooded his body. This was pure, aura energy, an energy that he could use to forward his own goals.

Eberus now understood why this tree was well guarded, the power inside it could be used for any purpose. At the minute, the aura was pure, but what would happen if he found the core of this power source and used his own aura to taint it. Would the aura inside the change to his own, and if so just how much power could he absorb. Eberus and his Lucario navigated the maze of tunnels inside the tree. Anyone else would have gotten lost, however, due to his aura power he was able to navigate and home in on the largest power source. The higher they got, the more power Eberus could sense until they came to a large cavern and in the middle of it was a large crystal formation, and a large lump of crystal rose up from the middle. On closer inspection inside the crystal, a human shape could be seen. Eberus knew who Sir Aaron was, and he laughed at the fate of the powerful aura user. So this is what had happened to him. Eberus could see the crystal were ciphering energy from Sir Aaron.

Eberus removed his glove and laid his bare hand on the crystal causing it to crackle as his dark Aura mixed with Sir Aaron pure aura. The power of opposing forces fought until eventually Eberus' power overloaded the pure aura and the crystal started to turn a dark red mixed with black. Eberus laughed as his tainted aura started to travel around the chamber and fill the crystal vines leading out of the tree and into the earth itself.

"Abandon me, will you? Well, let us see how you like having something taken away from you. I will taint your precious earth and destroy it. Then you will know my pain. So carry on hiding, sending your pathetic lap dog Ketchum after me. Each day I grow stronger, and soon I will be even strong enough to tear apart your dimension."

Hall Of Legends

The God Pokemon looked on as Eberus corrupted the Tree of Beginning. His corruption was reaching out to everything. Trees and the terrain around the affected areas began to die and change color. Eberus was trying to destroy everything that he loved. Arceus knew Ash was on the way, but he had foreseen all this. It was time for Ash to receive a major power boost, and the Tree was the key to that boost.

A/N Hey, Hey I am back after a very long break XD