On the Southern Island, Latias hears the melody of the Eon Flute, and tells her brother that Emerald has come. The two emerge to meet up with the person who plays the Flute, but as they get close, Latios realizes that it is someone else. Latias assumes the form of a girl wearing park ranger clothes as she approaches the boy, and soon recognizes him as Ruby. Ruby is glad that Latias remembers him, and hopes that she wouldn't mind him checking out something he has wanted to ascertain for a long time. He reaches out his hands towards Latias, and comes into contact with a surface that resembles the shape of her true form rather than what appears to the eye. He finally realizes that Latias's down is just like glass, which enables her to refract light and seemingly change her appearance.

Latias giggles that Ruby's touch makes her feel ticklish, and the boy quickly withdraws his hands, voicing out his apology. Latias reverts to her true form, and Latios remarks that she shouldn't let her guard down so easily. However, Latias thinks it is fine since Ruby is a friend of Rald's, and they have be considered comrades to certain extent after their fight together at the Battle Frontier against the sea monster.

Latios approaches Ruby and asks if there is something he wants, but before the boy could say anything, Latios already understands and wagers that something out of ordinary is happening again. Ruby replies with a nod, and Latios agrees to help. Ruby states that there is somewhere he wishes to go, and Latios decides to give him a ride. Telling Latias to wait on the Southern Island, Latios goes airborne with Ruby and quickly speeds off.

While in the air, Latios wants to know if Ruby has brought the item, and Ruby is shocked that Latios knows. Latios reveals that he and Latias also carry theirs, and thinks it is inevitable. After all, they obtained the items around the same time humans did. Ruby contemplates on Latios's words for a moment, and proceeds to strap on a silver bangle on his left wrist, which is known as the Mega Bracelet.

Meanwhile, at Dewford Town, Sapphire, Emerald and Steven are commanding Chic, Sceptile and Mumu to use the ultimate attacks. However, Ultima is far from pleased by their performance. She barks that one cannot just unleash the ultimate attacks in such a casual manner, and says it requires the precision of threading a needle. For Blaze, it needs to erupt like an inferno; for Torrent, it needs to stream like a flood; and for Overgrow, it needs to slash like a thorn. She states that a trainer cannot simply leave it to the Pokemon to wield the attack but must give accurate directions on the target, power, speed as well as angle.

Ultima soon gets fed up with the way Chic, Sceptile and Mumu are attacking, and yells for everyone to stop. She hollers that they failed completely, and while it is somewhat understandable for Steven since he is commanding someone else's Swampert, there is no such excuse for the trainers of Blaziken and Sceptile. She admits that their current skills may suffice under normal circumstances, but are a far cry from adequate for their current situation. She states that Blaziken, Swampert and Sceptile all possess the ability to undergo Mega Evolution, which is an evolution that goes beyond evolution. Although she herself knows little about the phenomenon, it enables a Pokemon to wield greater power, and it's not hard to imagine the tremendous amount of control it takes to wield the ultimate attacks on such a basis. She fears that Steven might have overestimated the strength of the young ones, and mocks that their feat at the Battle Frontier might have been due to the work of their seniors after all.

Sapphire and Emerald's prides are clearly hurt by the remark, and they quickly make another attempt to command a Blast Burn and Frenzy Plant from Chic and Sceptile, making sure to exercise more control this time. Ultima giggles that things look much better now, and Steven also tells Swampert to practice its Hydro Cannon. He then excuses himself from Ultima, and beckons his Beldum, Iron, to come along as he contacts his father.

Out in the sea, Joseph Stone answers Steven's call, and is glad to finally hear from him. He explains that he is currently with Briney and Drake on board the S.S. Tidal, which has docked near the shore on sea Route 134. The President of the Devon Corporation finds it amusing that the three devil kids of the sea are grouped together again, and wants to know if Steven has assembled the trainers he had his eyes on. Steven replies that he has, and introduces them one by one to his father: Ruby, son of the Petalburg Gymleader, whom Joseph recalls as the boy who is raising his Castform; Sapphire, daughter of Prof. Birch, whom Joseph remembers as the girl who delivered his letter to Steven; and Emerald, whom Joseph never met but is assured by Steven to be a powerful trainer since he conquered the entire Battle Frontier.

Steven states that the three trainers helped to solve the clash between the 'land' and the 'sea' which previously shook the entire Hoenn, and also put on end to the Battle Frontier incident that took place one year later. Joseph thinks they sound promising, and Steven reveals that the three were actually reluctant at first. As of now, the young trainers are being tutored on the ultimate attacks from Ultima, whom he invited over from the Sevii Islands. However, for Ruby, due to being occupied by something else, he will be arriving late and thus only his Pokemon is taking part the special training at the moment.

Joseph changes to a serious tone, and wonders if Steven has told the three what is going to happen to their planet. Steven states that he hasn't been specific, and reveals that he hasn't informed them of the aim and method of their special training either. Joseph decides that he will tell him himself, and Steven promises to contact him again once Ruby arrives. Before he hangs up the call, he sends over a photo he took of the Granite Cave's mural painting, and wants his father to have a look.

After Joseph ends his conversation with Steven, Briney gives him a friendly strangle, calling him Joey, and grins that his son is really dependable. Joseph giggles in response, and relents that as a father, Steven will always be an undependable son. However, Drake disagrees, and thinks he is a man with great leadership with composure and broad perspectives, just like his father. Joseph blushes at his old friends' compliments, and says they should perhaps take a look at the photo of the mural Steven sent over.

The three men gather around Joseph Stone's handheld tablet, and all feel a sense of bewilderment and nostalgia as they gaze upon the ancient portrait of Groudon and Kyogre, since the scene almost resembles what happened in front of their eyes back then. On a closer look, Joseph puts on a frown, and points out that what intrigues Steven are the mysterious 'alpha' and 'omega' symbols on the titans. However, what really catches his attention is the entity that seemingly cuts in from the sky between Kyogre and Groudon, which also has a 'delta' symbol drawn on its head…