Standing on the edge of the lake which spring water has a mind calming effect, Ruby is barely able to control his anger, and demands a confirmation from Juan that the Red and Blue Orbs which they have knocked out from Maxie and Archie are now inside the bodies of him and Sapphire.

Juan wants to know what made him think that, and Ruby pulls out the diary which Plusle and Minun always bring along with them, even back when they first met on the abandoned ship. He explains that the diary belongs to the owner of Plusle and Minun, who has invented an item called the Scanner, a device capable of tracking down the location of the Red and Blue Orbs.

It turns out that this person has also done a vast amount of research on the orbs and have put down all his findings in the diary. As written in the diary, the two jewels possess not only the ability to cause the ancient Pokémon Groudon and Kyogre to go into rampage, but also hold the powers to calm them. In order to elicit these powers however, it must be through what are referred to as the 'commanders'. Not only are the orbs known to assimilate into the bodies of the 'commanders', but there are also instances where the orbs would select their own 'commanders'.

Juan listens silently as Ruby speaks, and the boys says while Juan has acknowledged the fact that the orbs have been knocked out from Archie and Maxie back in Sootopolis, he didn't mention about the fate of the jewels. Yet after reading the diary, Ruby has a vague idea of what happened. When the orbs left the bodies of the evil teams' leaders, they immediately sought new trainers as their 'commanders'. It so happens that he and Sapphire were the closest at that time, and the orbs naturally selected them.

Ruby admits that he wasn't aware of that until he notices the symbols on the back of their hands while having their training on the island, but he is more than convinced about his theory as he remembers seeing the same patterns on Archie and Maxie's bodies back at the Seafloor Cavern.

Juan lets out a deep-hearted laugh and applauds, complimenting on Ruby's logical thinking with the French word bravo. He states that the boy has guessed everything right, and says he is truly impressed. But Ruby is less than amused. He hollers that it is a serious matter, and demands to know why Juan didn't tell them earlier.

Juan plays with his own moustache, and is surprised that Ruby hasn't figured out the true meaning behind his current mind training with his intelligence. Ruby doesn't understand what he means, and Juan suggests continuing their training right away. Calling together Zuzu, Nana, Coco and Popo, Juan tells Ruby to focus his thoughts on expelling the orb from his body, and wants his four Pokémon to synchronize their mind with Ruby on the same thing.

Ruby closes his eyes for concentration, and soon experiences a surge of energy through his body. Zuzu, Nana, Coco and Popo shut their eyes to focus as well, and Ruby instantly feels something rippling through his left arm. With a little encouragement from Juan, Ruby sends all his thoughts towards his left hand, and finally manages to propel the Red Orb out of his palm.

With his hat shaken lose by the powerful energy fields generated from the process, Ruby clutches the mystic jewel in his hand, and pants to catch his breath. Juan roars in laughter, and congratulates Ruby for his success, stating that he has achieved the true aim behind the training on the Mirage Island. The man then shows Ruby the Sandshrew timer, and says they have in fact one day left for training, as the island's time pace will soon synchronize with that of the outside world, and they must return to Sootopolis by then.

After Ruby and Sapphire heads back to the final battle ground, only one thing is required of them, and that is to stop Groudon and Kyogre by acting as the 'commanders' of the Red and Blue Orbs. Juan warns Ruby that for individuals who have a weak mind, they may be overwhelmed by the powers of the orbs, and actually get controlled the other way round by the ancient titans, which was the case with Archie and Maxie. He wants Ruby to keep his mentality strong all the time, and the boy nods in understanding.

Juan then remarks that while Ruby thought the Red and Blue Orbs selected them because of their close proximity in Sootopolis, he actually believes that it was more than a coincidence. In terms of strength and battle skills, Ruby and Sapphire are clearly not the best in Hoenn. If the orbs were seeking for powerful trainers, the gymleaders, Elite 4 or even the Champions would have been better candidates. That is why he is certain that the jewels picked them deliberately, and they are the chosen trainers to stop Hoenn's current catastrophe.

Finally, Juan reveals the reason why he didn't inform Ruby and Sapphire about the orbs right from the start. If they knew all along that the main aim of the training is to help them learn how to assimilate and propel the orbs in and out of their bodies under their own command, the thought would have plagued their minds, and hindered their progress in training. On the other hand, if they first focused on strengthening themselves physically and mentally, mastering the skills to control the orbs would come much easier.

Juan tells Ruby to take a rest himself before they resume training later, and leaves the boy on his own by the lake. While walking past the tree Sapphire is slumbering on, Juan steals a glance at the girl, and knew Ruby deliberately confronted him about the orbs when Sapphire was asleep so as not to shock her with the revelation. Musing to himself how Ruby not only has the battle skills but also the qualities of a gentleman, Juan puts on a content smile and walks off with his Luvdiscs.

After Juan leaves the scene, Ruby slowly climbs up to the tree branch where Sapphire is, and wonders if she is still asleep. However, it turns out that Sapphire has waken for quite some time now, and actually overheard his entire conversation with Juan. She tells Ruby that she has developed very sensitive ears after spending so much time doing field work in the wild, and Ruby in fact isn't too surprised about it.

Sapphire takes a look at her ungloved right hand, and sees that the Kyogre symbol is indeed glowing on its back. She seems lost in thought for a moment, but suddenly realizes that Ruby might feel guilty from revealing the news to her that way. She quickly assures the boy that she doesn't mind, as she would have known sooner or later some way, and Ruby remarks that accepting the truth is one thing, but they still must polish the skills of their Pokémon further and time is running out.

He pulls out his Pokédex to check on the attack lists of his Pokémon again, but there appears to be a signal interference, and the device only shows a disturbed screen. He wonders why the Pokédex has been acting weird since they arrived on the Mirage Island, and Sapphire suddenly notices something on the left side of Ruby's forehead which is normally hidden by his hat but is now uncovered since the hat was shaken loose earlier.

Ruby bolts with a start when he realizes Sapphire's staring, and quickly pulls hi hat tight. Just then, Juan returns and announces that they must resume training, and the two swiftly jump down from the tree.

For their remaining 24 hours on the island, Ruby and Sapphire alternate their training between double battles and calming their mind at the lake. As the sand in the Sandshrew timer falls quicker and quicker, the two young trainers get better and better with controlling the orbs. In no time, they could freely assimilate and expel the jewels in and out of their bodies under their own will.

When the sand in the Sandshrew timer finally tumbles down like a column, Tate and Liza rush to Juan and inform him that the time has come. Rain clouds start to loom over the skies of the Mirage Island, and powerful winds begin to blow. Juan states that the island's time pace is about to change from extremely slow to extremely fast, and it shall synchronize with that of the outside world during the short transition in a moment.

Meanwhile, at the Sky Pillar, old man Ghem is looking out to the stormy seas through his binoculars. To his surprise, the silhouette of a solitary island gradually materializes out in the emptiness, and he gasps in exhiliration that he is seeing the Mirage Island.

Back on the Mirage Island, Ruby and Sapphire are preparing to depart. Juan congratulates the two for completing their training successfully, and acknowledges the fact that Sapphire is doing gym challenges across Hoenn. Speaking on behalf of Tate and Liza as well, he states that the performance she showed has earned her the same recognition from them as she would in winning a gym battle. He grants her the Rain Badge of the Sootopolis Gym, while Tate and Liza reward her with the Mind Badge of the Mossdeep Gym.

Sapphire says her thanks while Tate and Liza help her pin the badges on her backpack, and Juan warns Ruby that the exact timing is crucial for their departure. He states that he together with Tate and Liza shall remain in the center of the island to monitor the time, and when the island's time pace matches exactly with that of the outside world, his Kingdra will give them a signal by creating fireworks with its water blasts. At that instant, Ruby and Sapphire must take off as soon as they can.

After making sure that Ruby and Sapphire understand the plan, Juan, Tate and Liza voice their final encouragement and return to the center of the island. Ruby and Sapphire stand amid the strong winds and heavy rain, and wait patiently for Juan's signal. Suddenly, Sapphire puts on a serious look, and says there is one thing she wishes to confess to Ruby before they leave...

Thanks To Coronis For Writing this for us