On the bowsprit of Sea Mauville, Emerald finishes emptying his bladder and groggily pulls his pants back up. He gets ready to go back to bed, but as he turns around, he comes face to face with a mysterious golden ring that floats in midair, which apparently encircles some kind of portal. A tiny pair of hands materializes on the edge of the golden ring, but when Emerald tries to reach out to them, they suddenly strike out to hit him on the head.

Fully awake now, Emerald cries out in bewilderment, and wonders out loud if it is a Pokemon that he is dealing with. He hurries back into Room 1 where Sapphire is still sleeping, and quickly snatches up his Pokeballs as well as his E-shooter. He sends out Sceptile as he goes back outside, and sees that his opponent is some kind of floating humanoid creature with two horns. Yet, as it is night time, he can only catch the silhouette of its outline hovering behind the golden ring.

Emerald tries his best to figure out the creature's birthplace and where it resides, and decides to try the soil of Sea Mauville. He inserts the capsule into his E-shooter, and fires off a barrage of bullets onto the ground beneath the Pokemon, creating a diamond-shaped pattern. Green light shimmers from the pattern, and at that moment, Steven rushes out onto the deck, stunned by what is happening. He asks Emerald what it is fighting, but Emerald says he has no idea either, since he doesn't recognize the silhouette of the creature and has never seen anything move like that before. Just then, the creature leaps away from the soil-lined seal to strike out again, and knocks back Sceptile while causing Emerald and Steven to tumble sideways.

Emerald is astonished that the soil didn't manage calm the Pokemon, and wonders if it doesn't originate from Sea Mauville after all. Steven sends out Metagross, and tells Emerald to leave the fighting to him as they couldn't risk exhausting Sceptile who has a much more important task to fulfill. He places two fingers on the Keystone at the tip of his lapel pin, and calls upon its powers to link with Metagross's Metagrossite. In a flash of rainbow light, the iron leg Pokemon Mega Evolves. It proceeds to deliver a Metal Claw, which narrowly misses the silhouetted Pokemon. Emerald exclaims that he has never seen Metagross in this form, and is intrigued that Steven holds his Keystone differently, which Steven explains to be his Mega Stickpin.

Steven soon notices that the mysterious Pokemon has managed to dodge every one of Metagross's attacks, and agrees with Emerald that he has never seen any creature move with such agility. Emerald decides to try the E-shooter once more, and picks the capsule of the Faraway Island. He fires off his gun to make another diamond-shaped pattern underneath the silhouetted Pokemon, but as green light shimmers around it, it simply grins and vanishes in a blinding flash in the next instant. Hiding himself behind a wall, Joseph Stone watches the scene in silence and keeps himself in the shadows. Unaware that Joseph is just around the corner, Steven wonders if they are encountering yet another new threat, and thinks he needs to report to his father. However, he thinks his father would tell him to just focus on dealing the asteroid and the Draconids.

Steven picks up one of the soil bullets from the E-shooter, and recalls having heard that Emerald has the special talent to 'calm' rampaging Pokemon by using the bullets to carve out a seal. He sees that the bullet is nothing more than soil balls linked up by pieces of thread, and wonders how the trick really works. Emerald explains that he has the ability to tell the birthplace and habitat of a Pokemon simply by looking at them, and his E-shooter is used for firing off soil from the location he identified. Steven realizes that Emerald is essentially using odor that is familiar to a Pokemon to calm its senses, and Emerald admits with a nod. However, he has failed to identify the birthplace of the Pokemon they just fought, and more alarmingly, not even the Faraway Island's soil managed to calm it. Steven wonders why it is unusual, and Emerald explains that it is the hometown soil of a Pokemon called Mew, which can be regarded as the ancestor to all Pokemon. In other words, soil from the Faraway Island should evoke the sense of home for all Pokemon, but it clearly didn't work on the mysterious Pokemon.

Steven takes time to ponder on Emerald's words, but the boy actually has other concerns. He wonders if they are really dealing with one Pokemon only, and Steven gets baffled by the remark. Emerald explains that while he was fighting the mysterious Pokemon, although there was only one physical entity, he has felt the gaze of another being, and it came from within the golden ring which the Pokemon held.

At the Sky Pillar, Ruby gets on board Latios, and the psychic dragon asks if he has finished what he came for. Ruby states that he has, and says apart from checking on all 49 floors, he has also taken snapshots of the giant mural painting. Latios wonders what they should do next, and Ruby replies that he plans to meet up with Steven and tell him of what he heard from Zinnia the night before. With that, Ruby activates his Keystone, and Latios begins to go into 'Soar' mode as it Mega Evolves. On their way up, Ruby sees that on the tower's 50th floor lies a row of heavy chains. In the middle of the room, there is also a circular pattern on the ground, and Ruby recalls that in order to reach Rayquaza at the Sky Pillar, a signaler must work on the chains to activate them while an intruder, who must be a child, enters the summit via the circular portal. 4 years ago, his own father and his friend Wally worked together to reach the summit where Rayquaza slumbered. Just now, Zinnia mentioned that she is the one authentic Successor of her clan who could save the planet, and said that the Sky Pillar was built by her ancestors. Moreover, 9 years ago, she tried to free whom she called the dragon lord, which was clearly Rayquaza. Putting the whole picture together, Ruby starts to see a connection, and secretly wonders if the method passed down by Zinnia's people to save the planet involves Rayquaza after all.

Mega Latios notices Ruby's contemplative look, and wants to know if he is thinking about what Zinnia said. Ruby grins that Latios is really intuitive, and the psychic dragon is curious as to how Ruby learnt of the woman since it was clearly his first time meeting her. Ruby responds with a grin, and explains that he became aware of her existence shortly after Steven told Emerald and him about the planet's crisis and the threat from the Draconids…

Agreeing to help only if Sapphire is not to be informed of the asteroid, Ruby leaves Steven with no choice but to agree to the condition. Afterwards, Ruby and Emerald sit along the shoreline of Mossdeep, and share a long conversation on the matter. Emerald asks if Ruby would also keep the news a secret from others close to him apart from Sapphire, and his question leaves Ruby speechless. The fact is, he knows that anyone who learns of such bad news would get into major despair, and it isn't something that he wishes to see. He thinks hard on whom to talk to and share the news with, but while the faces of his parents, his teacher Wallace, Wally and Prof. Birch all flash across his mind, he couldn't really bring himself to cause misery to any of them. Emerald sighs that he feels the same way, and wishes not to see the looks of despair on the faces of Crystal and the Trick Master either. Should they fail or succeed, he thinks it would be better if it goes untold.

At that moment, Ruby suddenly recalls the words of Team Magma's Courtney, and remembers her saying that anyone would do something silly for the sake of the person most important to them. He wagers that if it is Courtney, she would probably be able to handle the truth, and wonders where she is and what she is doing now. He reaches into his bagpack for the Memory Firelighter Courtney gave him, which allows Team Magma members to share their memories, and debates on whether or not to pry into her old memories beyond those involving his father at the Mossdeep Space Center, something which he has refrained from doing so all this time. Getting a hunch that he would learn something important, Ruby invites Emerald to watch together with him, and activates the Memory Firelighter.

As the images play, they see captures of Courtney at the Rusturf Tunnel, the Desert Ruins, Slateport City's Contest Hall, as well as on the Abandoned Ship. It then shows what appears to be an internal conflict, and they soon realize that Courtney was confronting a spy she found in Team Magma. In the scene, the female Grunt revealed herself to be a young woman with short black hair wearing mid-thigh length stockings, and tossed her uniform onto Courtney, feeling grateful that she didn't have to stay in the smelly clothes anymore. A Whismur named Aster ran up to the woman, who gave it a hug and found it cute as ever. Courtney angrily attacked with her Ninetale's Flamethrower, but the woman went airborne just in time with a Salamence. The woman then introduced herself as Zinnia, a descendent of the Draconids, and Courtney was surprised that she was not part of Team Aqua. Zinnia teased Courtney for not knowing about the Draconids, and said her ancestors were the ones who built the Sky Pillar. She mentioned that her intention of infiltrating Team Magma was to solve the planet's impending crisis, and since her work was done, it was time she made her departure. Courtney attempted to give chase on her Swellow, but Team Magma's leader Maxie appeared, and told Courtney to just let the spy be. After all, she has brought them countless valuable information, which included the existence of Groudon, its slumbering place, the method to awaken it, as well as the importance of the Orb which could control it. Maxie didn't care about intention behind the spy's actions, but as long as Archie didn't have the advantage, he would be happy. Hearing Maxie's words, Courtney decided to let things go as well, and the piece of memory ends at this point…

Mega Latios finally understands how Ruby learnt of Zinnia, and Ruby explains that he knew he had to meet the woman in person as soon as he saw the Salamence from the Memory Firelighter. Now that he has heard Zinnia's side of the story, it actually troubles him as to how he should relay the message to Steven, and Latios wants to know why. Ruby sighs that if Zinnia is speaking the truth, they and Devon should really just back off and leave things to her. However, it is expected that Steven and his father wouldn't be accepting it easily, as they clearly want to take the matter into their hands. Mega Latios is astonished that Ruby is thinking of backing off, and Ruby says it is only logical since the Draconids are aware of the asteroid 1000 years ago. The fact that they have also passed down the method to avoid the impact also means they have been making preparations for 1000 years.

Latios questions Ruby's acceptance of Zinnia, since it is now apparent that the incident 9 years ago which caused much pain to him and his father was part of her plan. Ruby sighs that he is indeed a bit angry about it, but thinks the two issues should be handled separately, since nothing matters anymore if their planet is going to be destroyed. On the other hand, if Zinnia really has a way to protect the planet from the asteroid crisis, he has no choice but to depend on her, although she has a bad personality, speaks with bad manners, carries a poor attitude, acts provocatively, never listens to others, and likes to brag. Latios sweatdrops that Ruby is clearly more than a little angry, and Ruby points out that while Devon views the Draconids' letter as a form of threat, Zinnia also regards Devon as her enemy, which indicates that both sides are antagonistic towards one another. Although he doesn't understand the reason behind, they really don't have time at hand for the two sides to battle it out. Ruby compliments Ruby for acting maturely, and Ruby says the only question is whether or not he can relay his message properly to both parties, and get them to see what he sees. Latios agrees, since things are never easy when one has a bad personality, speaks with bad manners, carries a poor attitude, acts provocatively, never listens to others, and likes to brag. Ruby wants to know what Latios means, but the psychic dragon brushes it off as nothing.

Suddenly, Mega Latios halts in its flight, and near throws Ruby off its back. Ruby clutches tight onto Latios and asks what is going on, and soon sees three Flygons approaching them, each carrying a man under their claws: a chubby bald one who also has a Sableye; a bearded one who has a Slowbro; and one whose hair covers his eyes and is accompanied by a Mawile. Ruby tells Latios to give way, but instead of passing through, the three men form a circle around him, and Ruby knows that he is their target, something which he had a hunch about when he first saw them.

The three men acknowledge the fact that Ruby has been to the Sky Pillar just now, and demand to know what he was doing there. They state that Ruby is going nowhere until he has given his answer, and proceed to call forward Slowbro, Mawile and Sableye to attack…