It is early morning in Hoenn. At the Sky Pillar, Ruby has set up a fireplace with twigs and boulders, and is making his special Berry soup in a pot he carries around with him. He offers some to Latios, but the psychic dragon politely refuses. To be frank, Latios is slightly surprised by what it sees, since according to Emerald, Ruby regards eating outside as a ridiculous act, not to mention the idea of camping out. However, the boy has set up camp in the partially crumbled tower, and is even cooking meals the primitive way.

Ruby states that he still believes that such things are ridiculous, but he has been forced to accept them as ways of life and has more or less grown accustomed to them. He reveals that 4 years ago, he and Sapphire had a joined birthday dinner celebration with their families. Out of elation from conquering all the Contest categories, he offered to accompany Sapphire in studying the wild Pokemon distribution for Prof. Birch. Unfortunately, that was delayed by the Battle Frontier Sea Monster incident. After the crisis was over, he became uncertain about his decision again as he thought of the prospect of living in the wild, but Sapphire insisted that he keep his promise and they eventually set out after the '10 Pokedex Holder Tournament' at the Battle Dome. Latios could see why it was hard for Ruby to stick to his beliefs, and Ruby says one doesn't have much choice in the wild. Despite that, the journey was actually very enjoyable. As he and Sapphire sailed on Lorry from island to island, visiting places they have never been before, meeting wild Pokemon they have never encountered before, they saw the richness and beauty of Hoenn's natural side, and the experience was really incomparable. Unfortunately, such richness and beauty may be ending in 10, or rather, 9 days.

Wearing a solemn look, Ruby recalls the night at Steven Stone's house in Mossdeep City, when the man revealed to Emerald and him the crisis that is going to befall their planet…

Emerald gaps his mouth wide open as he listens with disbelief that a giant asteroid is on its way to impact and destroy Earth. Ruby is stunned speechless at what he hears, and Steven states that while it is hard to accept, what he says is the truth. Currently, apart from him, this piece of information is only known to his father, President of the Devon Corporation, and a selected few. He reveals that Devon has already started working on a plan to avert the crisis, but it appears that someone who learnt of the information through unknown means disagrees with their scheme, and has issued a warning which threatened Devon to stop what it is doing. Nevertheless, they are at a stage where there is no time to spare, and they cannot afford to be thwarted by this kind of threat, which may very well evolve into a fight from the looks of things.

Ruby wishes to know what Steven wants from them, and Steven explains that he needs their power to prevent the asteroid from impacting their planet, as well as to fight the antagonistic forces that may thwart them. He states that in order to facilitate their work, he has prepared something to enhance their powers, and shows them a pair of silver bracelets, each embedded with a rainbow coloured stone. Without hesitation, Ruby straps a bracelet on, and Emerald is appalled that Ruby is accepting the item just like that. Ruby grins that it is not nice to reject gifts, especially when the stone embedded in it is so mysterious and beautiful, but Emerald protests that he is talking about whether they should believe Steven's claim of the planet's crisis and whether or not they should help.

Ruby raises a hand to pacify Emerald, and tells Steven that he would agree to help only on one condition. Steven is surprised to hear that, and Ruby acknowledges the fact that Steven is recruiting the help of all Hoenn Pokedex Holders. He wants to know if he also plans to contact Sapphire, who could not make it today since she is out studying the wild habitat, and Steven admits that it is his intention. Ruby hopes that Steven wouldn't tell Sapphire about the planet destruction part if it is the case, and simply say their help is needed to fight an enemy who is a threat to the Devon Corporation, which is the condition he speaks of. The boy then stands up to leave his seat, and Steven, despite being uncertain of the purpose behind Ruby's request, agrees to the condition…

Ruby admits to Latios that he was actually doubtful of the crisis when he first heard about it, but Zinnia has said the exact same thing, which means it is probably the truth.

Out in the open seas, Zinnia soars on her Salamence, and thinks back on her encounter with Ruby. She finds it a pity that such a smart and powerful kid is on the side of her enemy, and recalls the boy saying that his Mega Bracelet was given to him by the heir to Devon. She wonders how this heir came to possess the item, and whom it was that polished the Keystone into the form of the Bracelet. She grunts that Devon must have done it in their usual filthy ways, and grits her teeth in anger. Her facial expression draws concern from Aster, who calls out to her, and Zinnia apologizes for putting up a scary face. On a deeper thought, she thinks the issue is extremely minor compared with the crisis that is about to befall the planet, and decides to put it aside. She assures Aster that she is still herself, and since she has already issued her warning to their enemy, she should simply focus on their dragon lord and the mission that was bestowed upon her. Wearing a determined look, Zinnia gazes straight ahead and vows to protect the planet at all cost.

At Dewford Town, the sun has risen. Sapphire and Emerald continue to work hard in mastering the powers of Chic and Sceptile in their Mega forms, and are starting to get the hang of it. Steven soon intercepts to call for a break, and congratulates the two for successfully Mega Evolving their Pokemon for the first time. Emerald is still bewildered about the idea of Mega Evolution, and Steven states that both Blaziken and Sceptile have surpassed their previous limit to gain a new appearance. In other words, they have evolved beyond evolution and are now called Mega Blaziken and Mega Sceptile.

Sapphire is amused that a Blaziken is capable of further evolving, something which even her father is not aware, but in that instant, Chic glows with a soft light and suddenly reverts back to its usual state. Sapphire gasps in shock that it has returned to its previous appearance, and the same soon happens to Sceptile, which alarms Emerald as well. Steven tells them not to worry, and says Mega Evolution only takes place during battles. He decides to explain once more about Mega Evolution, and gestures to the circular rocks he gave to Blaziken and Sceptile earlier, which are collectively known as Mega Stones but have individual names. For instance, Blaziken's Mega Stone is called the Blazikenite, and that of Sceptile is called the Sceptilite. In order for Mega Evolution to happen, the Pokemon must possess the Mega Stone, but that alone does not trigger the phenomenon. The trainer must also possess a rock, which is known as the Keystone, and it is the rainbow coloured stone embedded on their Mega Bracelets.

Sapphire finds herself a little overwhelmed by the information, and mistakenly calls the wristband a Key Bracelet which is embedded with the Meganite. Emerald thinks she has it right, but Steven sweatdrops and says they got things a little mixed up. He wants to know how the two felt when they first strap on the Bracelet, and Sapphire recalls that there was a sensation of something flowing to it. On deeper thought, both Emerald and Sapphire simultaneously state that it is as if their powers and emotions were all channeling towards the Keystone. Steven grins that it is the right feeling, and explains that the Keystone is a rock that can gather the life force of humans, and subsequently react with a Pokemon who is holding a Mega Stone. He remarks that the basis of such a reaction is the bond between humans and Pokemon, and upon hearing that, Sapphire and Emerald both steal a look at Chic and Sceptile. Steven further elaborates that this is the reason why wild Pokemon cannot undergo Mega Evolution, and such a phenomenon is only observed in Pokemon who are close to humans and those who have trainers. Emerald realizes that it explains why the Pokemon reverts to its usual state after a battle, and Steven thinks he is right.

Steven turns around to ask what Ultima thinks, and the old woman doubts that she could have much meaningful input since it is her first time witnessing Mega Evolution as well. In terms of the ultimate attacks, she can see that both Blaziken and Sceptile have mastered the technique, and can control not only the power but also the accuracy in hitting small targets. Steven believes that it is time to proceed to practice the ultimate attacks in their Mega state, and Ultima agrees to it.

Sapphire shares a grin with Chic as she marvels at the power of Mega Evolution, and wishes that her father could see it as well. She pats the head of Mumu, who clearly wants to Mega Evolve as well, and wonders what exactly is taking Ruby so long. She relents that she shall teach Ruby about Mega Evolution when he arrives, and Emerald decides to keep his mouth shut on the matter. Sapphire then turns to Steven, and wishes to know more about the opponent that they are expected to fight, since they have already grasped the essence of Mega Evolution. Steven is impressed by her spirit, and shows them a letter which has the word 'Warning' written on it. Sapphire begins to read, but fails to get past the first sentence due to her subpar literacy. Emerald takes over to continue instead, and reads that someone is warning the Devon Corporation to cease their work on a wrongful technique, which is apparently called Infinity Energy. The writer warns that effort will be made to destroy Devon if they do not heed the advice, and signs the letter off as the Draconids.

Sapphire exclaims that it is clearly a threat letter, and Emerald wants to clarify that Devon refers to the company owned by Steven's father. Steven acknowledges it with a nod, and Emerald wonders what kind of opponents they are. Sapphire queries if they are an evil organization just like Team Magma and Team Aqua, but Steven says he isn't entirely sure. What he knows is that the Draconids are connected to meteors, and as their name implies, refer to a clan of people who live alongside dragon Pokemon. It is said that they are extremely powerful, and they are many heroic tales about them. Although they seldom show themselves openly in the major historical events, they are believed to have taken part and are opponents not to be underestimated.

Hearing that, Sapphire hollers that they shouldn't let their guards down simply because they have managed to trigger Mega Evolution, and claps Emerald hard on the back, causing the boy to choke. She declares that they should work even harder, and at that moment, Joseph Stone arrives with Mr. Briney and Drake and thanks the two Dex Holders for their dedication. Sapphire gasps in pleasant surprise at the sight of the Devon Corporation President, and says they haven't met since she rescued his Castform years ago. Joseph Stone thanks her for the help back then, and is glad to see her still so energized. Steven shares a handshake with Drake, hoping that Sidney, Phoebe and Glacia are all well, and Drake replies that they have all asked him to tell Steven not to be so engrossed in rocks and show his face sometimes. Meanwhile, Ultima and Mr. Briney both stick out their tongue to make a face, and tease each other for being older again.

Joseph Stone calls for everyone to get onto the ship immediately, and Steven is shocked by the sudden change of plan. He states that they have just gotten Gran Ultima's permission to try unleashing the ultimate attacks in the Mega forms, and his choice of words once again ticks off the old lady. Joseph frowns and says he doesn't want to repeat himself, and wants everyone to aboard the ship at once since Dewford is a populated town, and there is no way to ensure that information would not leak out. Mr. Briney and Drake explain that they have already found a place where the Pokemon could unleash their powers safely at will, and Steven soon learns that they are referring to Sea Mauville, a facility on the sea which has closed down decades ago and is currently a natural preserve.

Along the Lilycove coastline, where the Team Aqua Hideout used to be, Amber steps into the empty headquaters, and finds himself once again wandering back to this place. Donning a Fisherman's outfit now, he clutches onto his old headband which has the Team Aqua logo on it, and recalls that their organization's goal was to return to the Pokemon the sea which humans have contaminated. He thinks about his former comrades, Matt and Shelly, whose whereabouts are still unknown, and wonders why he keeps coming back even though there is nothing left, especially after he was abandoned by their leader and he himself has betrayed their organization.

Suddenly, something begins to materialize in front of him, and he soon sees Matt and Shelly waving at him. For a moment, his heartbeat raises in excitement as it seems that his former comrades have returned. However, a sweat runs down his forehead, and he quickly remembers that there was a man who could use flames to create illusions. Snapping himself out of his fantasy, he sends out his Gorebyss and orders a Hydro Pump. The attack instantly vanquishes the illusions of Matt and Shelly, and Amber once again finds himself alone in the room. However, a male voice then comes on to compliment on Amber's sharp senses, and says it is worth to wait at such a humid place after all. The voice states that their backstories are quite similar, and reveals that he is actually looking for a companion to fight alongside with. Since Amber can see through his illusions, perhaps he could consider joining forces with him.

With that, a man with blonde hair dressed as a Kindler shows himself with a Slugma, which is no other than the former Team Magma Admin, Blaise…