I don't own Pokemon or the idea of this story which I got from Captain Buggles. I just own my OCs.
TMs will exist in this universe but instead of replacing older moves I will just add to the list like TM02 is still Razor Wind while Headbutt is TM57. I will put a list of TMs in this universe on my profile and I'll just make the HMs TMs as well.
If you have a problem with me capitalizing words like Pokemon or Charizard deal with it because I always capitalize Pokemon and their names same with a good portion of extinct animals like Amphicoecelias and Uintatherium.
Later that night, Mew and Pikachu play about while Meowth sleeps. Pikachu smiles a bit, but it still cannot help the feeling of being separated from Ash. He puts down one of Mew's toys and looks out towards the horizon. As he says "Pikachu" out loud, Ash wakes up from his sleep and gets out of the Humvee the crew was sleeping in. He walks by, not noticing Lucario, who himself observes Ash looking towards the Tree of Beginning and saying Pikachu's name out loud.
The next day, they travel down the path, soon coming up to a stop. Lucario stands looking up at a cliff, the others wondering what is going on. Lucario tells them this was the spot that Aaron sealed Lucario in his scepter. He touches a Time Flower by accident and soon it replays exactly the same scene, when Lucario met up with Aaron, where Aaron renounced his loyalty to the Queen, threw his scepter down and sealed Lucario in the jewel. Then they watch Aaron fly off. Suddenly, from the two pathways on the road, the green army charges through the small pathway. Lucario appears horrified and begins throwing Aura Spheres at them, barely missing Ash in the process. Ash tells Lucario to stop because they are only illusions; Lucario does stop, shocked to have seen that event happen. Ash comes up to him, apologizing for his earlier words against him. Lucario accepts the apology, and makes Ash promise to never abandon Pikachu.
As they walk back to the Humvee, Lucario senses something. At the last second, he pushes himself and Ash out of the way just as a Regirock digs its way from the ground. It begins using Hyper Beam upon the "intruders". Lucario covers for them and keeps Regirock occupied before escaping into the crevice. Along the way Lucario tells them to make a turn at a tunnel. They follow the tunnel, and by now it seems as if they have lost Regirock. At the end of the tunnel, they come to a large cave of ancient Pokémon.
Now having made it into the Tree, the only way to get to Pikachu is by going up. Ash goes on ahead to another tunnel, followed by Lucario. Kidd takes out her specs, relaying information back to the company. Banks tells here that the tree is designed with many tunnels that form a network, like blood vessels. Kidd deploys out small helicopter gadgets to gather information about the Tree, then follows Ash.
The probes that Kidd deployed attempt to take samples of the crystal that lie there. However, a red blob engulfs and eats them. Kidd gets a warning that the probes are rapidly being destroyed, and that some sort of immune system in the Tree has been activated, which seeks out and destroys intruders. A Registeel becomes aware of the intruders and begins to hunt them as well.
At the end of the next tunnel, Ash finds himself outside, upon one of the "leaves" of the Tree. Ash calls out to Pikachu, who hears him and calls back. As things seem to turn for the better, a Regice stands in front of Ash's path and begins firing a barrage of Ice Beams. Lucario battles it while Ash gets away. He retreats to the tunnel, telling the others they must find another way because Regice is up ahead. Lucario throws an Aura Sphere at it to stun it long enough to get away.
They proceed through another tunnel, finding themselves at the cliff of a large hollow cave a good ways above the ground. Blue crystal pillars stick out from wall to wall. Deciding where to go, Jessie and James find themselves in the same place, at a different entrance. They jump down to Ash and company, landing with a crash. Apparently Regirock and Registeel found them. Lucario points a way, across one of the blue pillars that run like a bridge to another exit higher up. Lucario at the end of the line finds the three Regis on their tail. He fires an Aura Sphere at the bridge's center, destroying it before they have a chance to cross.
A red blob in the shape of an Aerodactyl, comes after them, but Lucario destroys it with his Aura Sphere.
Soon the red blobs approach from behind. The others try to find another way to get past them. One of them makes it through and almost catches Kidd, but Lucario gets in the way. The blob takes Lucario, but soon dissolves itself as the Tree does not consider Pokémon hostile.
The group soon discovers two Regis once again on their tails. As they run, they find a room with two tunnels. The group decides to split and meet up later. Brock, May, Kidd head down the right tunnel, and when Ash asks if Lucario is following, he says he won't leave until Ash finds Pikachu, knowing Ash would do the same for him. Ash thanks Lucario before sending out Grovyle and Corphish, using their attacks to slow the Regis down briefly before heading down the other tunnel.
Pikachu meanwhile continues using his senses to look for Ash, followed by Mew. As they begin to travel through another tunnel, three red blobs head by them. Those red blobs eventually reach Kidd's group, this time first taking Max, then Brock. Not wanting his Pokémon to go down with him, Brock releases Forretress and Swampert. Max sends out Shuppet May tries in vain to save her brother, who eventually disappears, at which point May is caught as well; she releases Combusken, Munchlax and Squirtle before she is gone; Kidd, on the other hand, manages to elude the blobs. Shuppet, Brock's and May's horrified Pokémon plus Bonsly are left behind staring at the places where their trainers disappeared.
ucario and Ash manage to lose the Regis, but they come up to a huge crevice with crystal pillars coming out from side to side. Not only is it a long way down, but strong gusts of wind blow from time to time. On the other side, Pikachu comes out from another tunnel with Mew still in the tunnel. Ash, happy to see Pikachu, runs out on the pillars while Pikachu does the same. Pikachu has no problem hopping from pillar to pillar in the wind, but Ash occasionally slips. He continues on when the wind gets too strong. Both him and Pikachu meet in the middle, where they jump to meet, though they soon fall down. In the nick of time, Kidd uses her grappling hook to swing across and grab Ash and Pikachu, landing at the tunnel entrance where Lucario is standing. Ash and Pikachu are finally reunited, and he introduces his partner to Lucario, who is now beginning to truly understand the deeper relationship that is possible between humans and Pokémon. Sceptile and Crawdaunt appear, then Mew shows up with Ash's hat appears climbing down the pillars. Now the group need to escape the Tree so travel as a group down the next tunnel.
While going through the tunnels, Ash asks what happened to the others. Kidd doesn't answer at first, making Ash realize that they were taken by the blobs. Kidd confirms this when they spot two more red blobs up the path. They quickly find a branch off to another tunnel but the blobs continue right behind them. The group comes to a room with large crystal formations. Lucario goes on ahead, but is ambushed by Registeel and Regirock. Registeel grabs him, giving the red blobs a chance to capture Kidd and Ash, which is what is intended. As Kidd gets "eaten", she releases both her Weavile from their Poké Balls. Lucario desperately tries to free himself, but it stunned by Registeel. Ash releases Donphan and Swellow and tells Pikachu to look after the others. Pikachu, desperate to save Ash, grabs onto his hand and is assisted by Sceptile and Donphan with Crawdaunt and Swellow watching and supporting them to save Ash. Lucario manages to free himself from Registeel's grip and hurries to help, but it is too late: Ash is gone as the blob slips into the ground, and the crystals turn blue again. Ash's Pokémon, devastated by their loss, begin to cry. Lucario watches this, appearing hurt as well.
Mew sees how upset Pikachu is from losing Ash and flies up, touching a crystal. It begins to glow green, as well as every crystal in the area. Soon the blobs, now green, form up into mounds and dissolve away, leaving their victims behind, alive and well, just where they had been taken. As Ash is also released from the blob, Pikachu jumps into his arms and is quickly followed by Donphan and Crawdaunt with Sceptile and Swellow watching as all are overjoyed to have him back. The Regis walk off, not seeing them as a threat anymore. Lucario tells Ash that Mew communicated to the Tree and was able to convince it the humans were not a threat. Ash thanks Mew for saving them as Mew tries to return Ash's hat again, but it drops the hat and floats down - being caught by Kidd - and is now very weak.
Suddenly, all of the crystals turn red in color. Kidd's boss says that the tree's immune system has gone into shock and the entire Tree has become unstable. Kidd tells Ash that Mew and the Tree are connected and if the Tree is destroyed, Mew will certainly die. The crystals begin to blacken and crumble and parts of the ground collapse. Ash returns his Pokémon to their Poké Balls and, with no time to lose, Mew signals and leads the group to the core room.
In this room, Lucario looks to the side and notices that there is a crystal formation with Sir Aaron's body inside it. Lucario does not understand why Aaron is here, but sees his gloves nearby. Ash finds a Time Flower next to the core and runs up to it to activate it. When the pod opens up, it displays the scene as Aaron comes in. Ho-Oh also comes in, revealing itself to be Mew. They watch as Aaron begins delivering his Aura, the only energy that would suffice, to Mew. Mew stores the power and once enough has been stored, goes to the core to begin the Tree's restoration. At the end, they see Aaron stumble and fall and the scene ends.
Lucario realizes that Sir Aaron did not abandon the kingdom, but in fact sacrificed himself to save it and that he is truly the hero everyone believes him to be. Lucario is filled with guilt for doubting his master, but realizes that the power of the Aura can restore the Tree again. Lucario, seeing how he can utilize the Aura that Aaron can, declares he will be the one to do it. Lucario goes up to Mew and begins transferring energy, but is soon pulled back. He realizes he is not strong enough yet to deliver the energy needed. Ash remembers that Lucario mentioned he had the same Aura as Sir Aaron, and can control it as well. He puts on Aaron's gloves, which help to channel the energy. Kidd tries to stop Ash, telling him he would be sacrificing himself, but Ash explains that if he doesn't help, the Tree (as well as Mew and all the other Pokémon living in it) would die. Both Lucario and Ash begin channeling energy into Mew. As time passes and they channel more energy, it begins to strain them. Lucario looks at Ash and, at the last possible moment, pushes Ash out of the way, telling him he'll take it from there. The energy channeling completes and Mew swiftly moves to the energy core of the Tree, the stored energy releasing a green light that restores life to the Tree. The crystals turn green and emit bright beams of light across the land as well as in the castle. Down one of the tunnels, Jessie and James note that they've somehow managed to survive, as Meowth finds them and the three friends are happily reunited.
Kidd confers with Banks and finds out that everything is normal. Lucario stumbles down next to Aaron's crystal, exhausted and in the same condition as Aaron when he collapsed. Lucario's hand bumps into a Time Flower, activating it. This one shows Aaron sitting there, saying his last words. He tells Lucario that he only sealed him up because he knew Lucario would follow him no matter what otherwise. He also says that Lucario was not his servant, but his partner and friend. Lucario sobs a bit and smiles, understanding now Sir Aaron's sacrifice, and apologizes for failing him, but Ash assures him that it isn't true and Lucario has proved himself to be a True Guardian of Aura as well. Lucario thanks Ash and then starts to disappear. Ash begs him not to die, but Lucario tells Ash its all right as Sir Aaron is waiting for him as he goes, turning into an orb of energy that combines with Aaron's energy and floats up to the sky at the same time causing Aaron's crystal to disappear.
Brock, May, and Max step outside to see the Tree is normal again as Kidd and Ash step outside from a nearby tunnel. Kidd gets in touch with Banks, who tells Kidd that she will make a fortune from the information she has gathered. Kidd however decides not to publish this adventure and says to keep it a secret, stating that the Tree would be ruined by tourists, and Banks reluctantly agrees as everyone else sadly ponder Lucario's sacrifice. Ash, knowing that he will never forget his friend or the relationship that is possible between humans and Pokémon, states that Lucario's aura is with him.
They find out the tapestry in the castle showing Aaron holding up his scepter has changed; it now includes Lucario, Aaron's partner and friend, standing beside him. Ash and company take a cable car down. Along the way they see Kidd waving from her Humvee before leaving. Bonsly remains with Mew at the Tree of Beginning, both of them thrilled to have found a friend. Ash and friends travel in the town below the castle. In what would appear to be the afterlife, Aaron and Lucario are shown standing together. Aaron takes a bite of something and reacts positively; a closeup reveals a bar of chocolate like the one Max shared with Lucario earlier. Ash and his friends travel towards a bridge and the next city, continuing their Pokémon journeys together.
