Hundreds of years ago

Lucario jumps from boulder to boulder to a spot overseeing a wide expansive valley. Lucario senses something and uses its Aura to see the entire landscape. Lucario lets his sight travel about, going over more rocks and hills until he sees a large formation of a gigantic, red-armored Pokémon army, mixed with human foot soldiers, that is charging towards the middle of the valley. He looks to the other side of the valley and sees an equally gigantic, green-armored army, with equally powerful Pokémon of different species charging to the same destination.
As Lucario is comprehending the danger of the event, three Houndoom from the red army arrive at the scene, which Lucario evades and leaps away. He heads to a crystal formation on the ground, touching it and then speaks through the crystal to his master, Sir Aaron, an Aura Guardian, who is at Cameran Palace. Aaron stands upon a balcony with Queen Rin that overlooks the entire land, and he hears Lucario's voice coming from another crystal formation on the balcony. It seems the palace is in imminent danger of being overrun; peace cannot be brought to the two warring sides.
The three Houndoom find Lucario and proceed to attack him. After being cornered, he is left no choice and fights back. Using his Aura to sense his surroundings (due to getting dirt in its eyes), he manages to defeat his pursuers.
Knowing that Aaron must leave, Rin explains she is obliged as queen to share the same fate as the castle. After their last exchange of words, Aaron hops a ride on his Pidgeot to the valley. Aaron tells Lucario that he has abandoned the palace and the Queen and will not be returning. Lucario cannot believe what he is hearing and implores him to wait, but Aaron throws down his scepter, which absorbs Lucario into a jewel at its top; from within the jewel, Lucario can see Aaron going off and feels betrayed by his master.
Rin observes from afar that the Tree of Beginning is suffering from the conflict. The two armies clash in the middle of the valley. Outside of the tree, Pidgeot flies away alone. With this, Ho-Oh returns to the Tree of the Beginning, revealing itself to be Mew.
Pidgeot approaches Rin with the scepter in its beak, which she takes. Suddenly, Rin witnesses the sight of the tree starting to glow green, and soon every crystal formation throughout the land emits a beam of green light. As the light spreads further out, the armies stop their battle, in awe of the event that is taking place.

Present day

And with that, a mother reads the story to her daughter. According to legend, Queen Rin believed Aaron to be the hero who had used the power of the Tree of Beginning, where Mew is said to live. The two armies stopped their fighting, their hatred replaced with understanding and returned to their lands and peace was restored. Aaron became known as the True Guardian of Aura, without whom peace would have not been restored. To this day, the legend is commemorated every year in the town of Rota and the same Cameran Palace.
AshMayBrock and Max happened to come to the town during this time, and decided to participate in a tournament to decide who will be the "Hero of the Year." Ash and company walk along a bridge to Cameron Palace. They are dressed in their regular clothes while the townsfolk are in renaissance outfits. Meanwhile, a Taillow overhead lands on a window of the Palace, turning into a Pichu. In another room, Ash and company finds a costume closet and decide to dress more appropriately. They later hurry to the tournament that is about to begin.
Before the tournament begins, Queen Ilene, the ruler of the palace along with her maid Jenny and her Pokémon Mime Jr., steps out to the royal box seat to officially begin the tournament. Ash andPikachu eventually win and Ash becomes the "Hero of the Year".
Ash then walks up to meet his opponent from the finals and is surprised to discover the Trainer is actually a girl. She introduces herself as Kidd Summers. Ilene then announces that there will be a ball and banquet in honor of the new "Guardian of the Aura". Ash is presented to sit in a throne that overlooks the ballroom. Ilene presents Ash with Aaron's scepter. He suddenly hears a voice from the jewel crying "Why?". A confused Ash asks if anyone else heard it, but nobody did. Shrugging it off, the ball soon begins.
With the new company, Mew (in the form of an Aipom) takes the Pokémon posse about through the castle. Meowth, who is helping himself to some food underneath the table, hears them and decides to follow them but is unable to. Mew directs the Pokémon to the attic directly above the ballroom chandelier and shows the Pokémon a few toys, which the group begins to play with. After a bit, Mew transforms from Aipom into Pikachu and begins dancing with Ash's Pikachu.
Kidd slips away from the ball into the same direction the Pokémon went off to. She quickly slips out of her costume, sporting a pink-purplish wetsuit-like outfit. She makes her way outside from the window, Meowth noticing and follows. She climbs up to the rooftop before shooting a grappling rod to a tower across the castle grounds. She jumps off from one roof to the next. Meowth only goes so far, before he slips down the sloped rooftop. His tail grabs a hold of a decorative steeple rod, but he ends up swinging down and crashing into a window, ending up in the attic where the other Pokémon are located.
Ash sits upon the throne, a bit bored. He asks if he could get some food but Jenny keeps him down on the throne, telling him to act like the hero, Sir Aaron. Max notices their Pokémon are missing, until he spots Munchlax nabbing a plate of fruit and going back upstairs with it; Max follows Munchlax to the top.
Kidd manages to get to a good vantage point on the roof where she can see through the broken glass Meowth made. She sees Mew and then puts on a pair of special glasses and begins reporting information to her boss, Banks.
In the attic, Mew takes on its original form, looking at Meowth to see if he is alright. Taking this chance, Kidd sends out two Weavile and orders them to place a tracking device on Mew. Both of them jump into the broken window and begin a swift attack at Mew. Mew dodges their assaults easily. In an attempt to stop Mew, both of them use Blizzard just as Mew flies towards the door. At the same moment, Munchlax comes into the room and finds itself frozen in a block of ice. The door also freezes at its hinges and cracks. Max arrives and finds the door hard to open.
Mew is soon held down though, and just when one of the Weavile is about to attach the tracker on Mew, Pikachu shocks the Pokémon with a Thunderbolt. Mew escapes to Pikachu, but the Weavile try another Blizzard attack. Both Mew and Pikachu dodge, the attack hitting the other Pokémon, freezing them. Mew then flies over towards Meowth who is at a corner, and transforms into a Meowth. Mew switches itself and Meowth around to confuse the Weavile, but Meowth speaks and ruins the plan. Soon Pikachu is left exhausted and weakened from battling with the Weavile.
Kidd notices this and figures that the plan did not go as well as expected. With Pikachu unconscious and the other Pokémon frozen, both Mew and Meowth are on their own. Mew transforms back to its original self. Max finally gets the door open, but only a crack as he watches what goes on. Mew soon teleports before the Weavile can do anything else. The three teleport to one of the tower's steeples, and then Mew transforms into a Pidgeot and flies off, towards the Tree of Beginning.
Lucario kneels down before Ash before realizing he isn't Aaron. Lucario becomes confused at what is going on, seeing the many people. Lucario soon escapes through the crowd of people, running around through the castle. He sees that it has changed, and memories of him and Aaron soon start replaying in his mind as he walks about.Back at the ball, Jenny tells Ash to stand up and copy the hero's pose as shown on the Sir Aaron poster. Once again Ash hears a voice from the jewel. The jewel soon glows, releasing Lucario from it. Lucario, still blinded from the Houndoom's attack during the great battle, is using Aura to see and mistakes Ash's form with Aaron's due to their similar Aura.
Lucario stops at a display room, which he remembers to be a bedroom. Ash, May, Brock, Ilene and Jenny confront Lucario in the room. Looking at Ilene, Lucario mistakes her for Rin and is glad to see her. Ilene says to Lucario that she is the descendant of Rin, the Queen who was reigning at the castle during his time. She goes on to explain that the memories that seem to him like yesterday, are in fact ancient events.
At the Tree of Beginning, Mew looks after Pikachu, who is resting in a bed of leaves. Meowth seems to understand what Mew is up to, seeing a large pile of toys that it has gathered. Pikachu soon recovers.
Back at the throne room, Ilene explains to Ash and company the story of Aaron and Lucario. Just then, Max runs into the room, exclaiming he just saw Mew getting attacked, and it took Pikachu and Meowth somewhere. Kidd comes out of the same door, confirming what Max saw. She also says that she saw Mew transform into a Pidgeot and take them away to the Tree of Beginning. Ilene takes them out to the balcony overlooking the land and shows them the tree, explaining that the tree is actually a unique rock formation, and supposedly possesses healing powers beyond imagination. It can revive the earth and soothe angry hearts, although it requires Mew. Ash decides the only way to get Pikachu back is to go over there himself. At Ilene's request, Lucario agrees to accompany the group in their quest.
Kidd says that she wants to go too. Brock reveals Kidd has been on a lot of major adventure fronts, including deep sea diving in a sub and space travel. Brock goes crazy about how much he wanted to meet her (with Mime Jr. impersonating vividly) and how it has been an honor. Kidd says that she is here for the adventure, and she has a Humvee that will get them there in no time. The next day, Kidd takes Ash and company towards the Tree of Beginning, Lucario running up ahead while Ilene and Jenny stay behind at Cameron Castle. Jessie and James stow away in the trunk.
Pikachu, after waking up, sees that it is with Mew and Meowth. Mew is excited that Pikachu is awake and well, playing around with it for a moment. Meowth falls into a hole concealed in a branch stump. Pikachu goes up to and pokes his head in along with Mew. They see a long vertical tunnel with green bubbles coming up. Mew hops onto a bubble, followed by Pikachu. At another branch stump up higher, the three Pokémon come out. They walk up to the edge of the land, seeing the magnificent landscape below them.
The crew takes a break for lunch. Lucario finds some Berries while he sits upon a boulder. As Brock passes out the plates to everyone a Bonsly takes one of them before he can get to it. Brock finds Bonsly below eating the lunch. Brock scolds it but this only makes it cry. May and Ash think Brock was too harsh, but Max points out that Bonsly is only using Fake Tears, and the Bonsly runs away with the food. Lucario picks up the plate, offering Bonsly a Berry instead. The Bonsly runs off behind a rock, peeking behind it once in a while.
They continue to travel down to the Tree of Beginning, but they stop once more. This time, the road is littered with geysers that are erupting and then May notices something off to the side, a hot spring! They decide to stop until the eruptions subside and take a dip. Ash, Brock, Max, and their Pokémon (except Phanpy) take a swim in the hot spring.
When May comes out of the Humvee from dressing, Bonsly drops upon her head from the roof who apparently took a ride with them, so May decides to take it along. She tries to take Bonsly into the water, but the small Pokémon jumps out and hides behind Phanpy. Max explains that Bonsly doesn't like water because it is a Rock Pokémon. Lucario sits upon a rock, remembering the time when Aaron took him here. The memory is interrupted when Ash told Lucario to jump in, but Lucario simply walks off, Ash a bit annoyed by his cold attitude. May notices a strange looking plant sitting high up on the rocks, and Ash volunteers to get it. As soon as he grabs it though, he slips and falls off. May catches the plant, which looks like a crystallized pod. Seeing as how it is a flower, they decided to plant it. Just before they do, the pod suddenly blooms and a holographic vision fills the area, replaying how Ash fell down the cliff as he was getting the plant. Kidd identifies it as a Time Flower, explaining that it records events in the area at the time it was planted and then it can replay the scene at a later time when activated by Aura.
Night later falls and they decide to camp for the night. Ash tells everyone the story of how he and Pikachu became partners and best friends while saving it from a flock of Spearow during the lightning storm. Lucario suddenly walks away in disgust, and when confronted by Ash, Lucario tells him of his belief that humans and Pokémon could never be friends. Ash gets very angry at this, and asks Lucario why they should believe everything he says about Sir Aaron anyway. Lucario asks Ash how does he know Pikachu was kidnapped, suggesting that maybe it just wanted to get away from a weak Trainer. This pushes Ash over the edge and he tackles Lucario, both rolling down a ledge to a pond. The two thrash about in the pond, the others coming to try to stop the two from fighting. Lucario finally throws Ash out to the shore, jumping off to the top of the ledge and walking off.
Lucario finds a tree to lean upon, recalling another memory of how Aaron trained him to master his Aura. Just then, Max comes up and gives a bar of chocolate to Lucario who, after some hesitation, decides to try it.
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 Beamupon 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 Regicestands 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.
As Jessie and James run up ahead, a red blob comes from the other side of the tunnel after them. It turns into a Cradily shape and swallows up Jessie. James tries to save her by sending out Cacnea, using Pin Missile, as the rest of the group appears behind him. However Jessie is eventually swallowed up. Another blob takes James, who then sends out Chimecho, telling it to save itself. The rest of the gang comes into view and sees the stranded Pokémon.
One more red blob, this time in the shape of an Aerodactyl, comes after them, but Lucario destroys it with his Aura Sphere. The gang are quickly on the run again, and Cacnea and Chimecho are left standing sad and confused over what happened to their Trainers. 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 and a very tired Meowth. As they begin to travel through another tunnel, three red blobs head by them, causing Meowth to wonder what they are. 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 Mudkip. May tries in vain to save her brother, who eventually disappears, at which point May is caught as well; she releases CombuskenMunchlax and Squirtle before she is gone; Kidd, on the other hand, manages to elude the blobs. Brock's and May's horrified Pokémon (plus Bonsly) are left behind staring at the places where their trainers disappeared.
Lucario 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 and Meowth 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. Grovyle and Corphish appear, then Mew shows up with Ash's hat and Meowth 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, and Meowth is upset when told that Jessie and James have also been consumed by them. 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 Phanpy andSwellow and tells Pikachu to look after the others. Pikachu, desperate to save Ash, grabs onto his hand and is assisted by the other Pokémon. 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 Ash's other Pokémon, all overjoyed to have him back. The Regis walk off, not seeing them as a threat anymore. Meowth 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. While Meowth hears James's voice nearby and hurries off unnoticed, 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).
During the credits, 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 while Team Rocket floats overhead, seemingly plotting another capture of Pikachu, but Wobbuffet knocks Meowth out of the balloon by accident, causing Meowth to cling to the bottom of the balloon. 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.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.


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