And so the deadly battle between the ancient titans Groudon and Kyogre at the historical city of Sootopolis draws to an end. Leaving this final battle ground, the land and sea titans now return to their long sleep underground. However, the location they choose to slumber this time is different from where they did that several hundred years ago.

At the Pokemon Association's giant airship, Ba.Goon, the monitor screen shows that the two titans have parted ways after leaving Sootopolis. While Kyogre is returning to the Seafloor Cavern, Groudon has picked a new location, and made its new home at the volcanic crater of Mt. Chimney.

Captain Stern wonders why it is the case, and the Association Chairman explains that Groudon and Kyogre no longer want of nothing from each other. In the battle they just had, both have fought to their fullest capacity, and have fulfilled their innate nature to challenge each other. In other words, no feud exists between the two titans anymore, and they have thus chosen to go separate ways.

The Chairman wears a solemn look when he thinks of the fact that Norman's awakening of Rayquaza became inevitable at the end, and lets out a little sigh. He then makes a public announcement to everyone on board the airship, and states that thanks to the combined efforts of their warriors: the gymleaders, who fought the evil teams' admins; the Elite 4 and the two Champions, who used Regirock, Regice and Registeel to prevent the destructive forces of Groudon and Kyogre from consuming the whole Hoenn; as well as the two trainers who challenged and knocked out the Red and Blue Orbs from the evil teams' leaders, they have claimed victory in their battle against Hoenn's catastrophe.

With both Groudon and Kyogre are gone, it is time to spread the good news across Hoenn, and let the residents know that they are now safe. However, in that instant, the Chairman receives an incoming call from Wallace, who informs him of the bad news that Steven has collapsed. The Chairman gasps in disbelief, and urges Wallace to take Steven to the hospital, but Wallace grieves that it is too late, because Steven is already dead.

Kneeling over his fallen companion on Registeel, Wallace trembles with pain, and wonders why it has to happen. He reasons that Steven's body is taking the largest toll among all of them since he was the leader who directed the Elite 4 to exert control over Regirock, Regice and Registeel, but still, the intensity shouldn't have taken his life.

Just then, Phoebe makes contact with everyone via the Pokegear, and sobs that she should have known better. She was standing right beside Steven when he lifted the seal from the ancient stone plate to free the legendary golems, and she remembers clearly two sentences carved on the tabloids which read 'But, we sealed the Pokémon away. We feared it'.

Sidney wonders if the ancient people's fear of the Pokémon was due to the dangerous risk in controlling them, and Drake believes that it was the case. He remarks that while Regirock, Regice and Registeel are not as powerful as the titans Groudon and Kyogre, like the titans, they pose threats to humans, just probably in a different way.

Tears start to well up in Glacia's eyes as well, and she points out that the 6 Pokémon lineup formed by Wailord, Relicanth and four Beldums which was maintained the whole time during the battle is starting to fall apart with Steven's demise. As soon as she says that, Regirock, Regice and Registeel begin thrashing around, and the Elite 4 and Wallace, with Steven in his arms, quickly hop off onto the ground. With the 6 Pokémon lineup broken, they no longer have control over the legendary golems, and the three ancient beings soon shoot off into the skies.

Shielding Steven from the swirls of wind stirred up by the golems' departure, Wallace takes another look at his fallen companion, and mumbles his name while the agony burns him up inside.

Meanwhile, on the ascended ground, Ruby continues to shake his unresponsive father, Norman, whose face and eyes are darkening by the minute. Suddenly, Rayquaza lets out a shriek, and goes into a rampage. It knocks Ruby and Norman down onto the ground with its long body, and with another howl, lifts off into the skies and disappears.

Ruby eases Norman against a boulder, and the man remarks with a weak grin that just like Groudon and Kyogre, Rayquaza is also an ancient titan, and it is impossible to fully control it. He believes that the sky dragon must be mad at him for waking it up from its slumber and bringing it to the final battle ground by force.

Ruby listens with a confused look on his face, and doesn't understand what his father is talking about. Norman grins that Ruby shouldn't be too surprised, because he should have known by now that the Red and Blue Orbs are the mediums used to control and suppress Groudon and Kyogre. However, for Rayquaza, such an item does not exist, and to forcefully control it without one will end up in the pathetic situation he is in right now.

Norman begins explaining to Ruby that several years back, the Pokemon Association has succeeded in capturing Rayquaza to study on it. The Association's researchers have even developed an artificial item known as the Green Orb to act as the medium to control the sky titan. Unfortunately, the item failed to work as effectively as the Association has hoped. Five years ago, on the day that Norman sat for his gymleader selection test, Rayquaza escaped from the Association's research building, and Norman was bestowed upon the task to find it afterwards.

Ruby remembers what he learnt from Courtney's fire lighter, that Norman was deprived of the right to sit for another selection test for 5 years and ordered to go after Rayquaza, and starts to see a clearer picture. However, he fails to understand why Norman received such a treatment, and reasons to himself that Norman must have done something wrong for the punishment.

But on a deeper thought, he knows well that his powerful father is not the kind to make mistakes, and wonders if it is possible that he is taking up the responsibility for someone else that day, someone who was also present at the gymleader selection test's venue.

As the memories of that day flash across Ruby's mind, he recalls the meeting with Prof. Birch and his young daughter Sapphire, how the sudden appearance of a wild Salamence stopped Sapphire and him in their tracks, how he battled hard to get rid of it, and how Sapphire cried afterwards out of fear.

But there was something more.

The Salamence ran off towards one of the buildings after being defeated, and shortly after that, a serpentine creature broke out from the ceiling of that building and disappeared into the skies, a serpentine being who looked just like the sky titan Rayquaza.

Ruby begins to tremble with disbelief as he realizes what really happened, and tears quickly well up in his eyes as he wonders out loud whether he was the one responsible for setting free Rayquaza. His tears drip onto the darkened face of Norman, and the man weakly confirms Ruby's suspicion. Indeed, the Salamence Ruby drove off that day barged into the research building of the Pokemon Association, and ended up freeing Rayquaza from its entrapment…

On that one day five years ago in Johto, Norman is getting ready to sit for his gymleader selection test. His good friend Birch has come over all the way from Johto to give his support, and Norman's wife is overjoyed that her husband could finally fulfill his long-time dream. Birch jokes that Norman's wife doesn't seem to have a single doubt that Norman would earn the title, and wonders which gym they would pick. Norman's wife giggles that she will follow wherever her husband goes, and Birch gives Norman a friendly nudge, teasing him as the luckiest guy in the world. He suggests that he join him in Hoenn, and Norman grins that he will consider it.

Norman then wonders where Ruby is, and his wife explains that the boy is having fun with Birch's daughter, Sapphire. Norman thus decides to get inside the arena building used for the selection test later, but his wife protests that there is still plenty of time, and wants to walk around some more. Norman has no choice but to comply, drawing a deep hearted laugh from Birch.

Suddenly, the three of them hear a loud shriek, and turn around to see a flat-roofed building not far from them trembling. Birch exclaims that it is the research tower, and Norman tells his wife to stay where she is, while he rushes over with Birch to see on what is going on. However, before they could reach the building, a serpentine creature bursts out from its roof, and lets out a deafening shriek.

Upon seeing Norman and Birch, the creature fires off a barrage of energy balls from its mouth, and Norman hurriedly calls out his two Slakoths to fend them off and counter back. This ends up infuriating the serpentine being further, and with another shriek, it whips its tail around to send Norman, Birch and the Slakoths flying. It then lifts itself away from the rubbles and shoots off into the skies, leaving behind a cloud of smoke around the research tower's collapsed rooftop.

Panting to catch his breath, Norman wonders what kind of creature it was, and Birch suggests they head inside the building to see if anyone is hurt. To their surprise, the first thing they see is an injured Salamence sprawled across the floor, lying right in front of a giant container which glass shield is shattered, and the electrical machinery attached to it badly damaged.

A wounded young lady wearing a lab coat soon emerges from the fallen cement blocks of the rooftop, and the two men hurry over to check on her. The lady wears a worried look on her face, and reveals that the creature which just escaped is powerful and special Pokémon studied and monitored by the Pokemon Association.

She remarks that their building has the best security system to ward off intruders, but they never would have expected a rampaging Salamence to barge in. Not being trainers themselves, she and the other researchers could only watch helplessly as the Salamence destroyed their machines, and ended up freeing their Pokémon under research from its restraint system.

While Birch explores more about the special Pokémon from the young lady, Norman turns around to inspect the Salamence, and notices various sites of injuries on its body. He wants to know if it hurt itself from colliding with the machinery, but the young lady recalls seeing it wounded already the moment it barged in.

Birch wonders what is wrong, but Norman remains silent, and takes a closer look at the dragon Pokémon's wounds. He recognizes them as damages inflicted by hyperbeam, irontail as well as confusion, and the pattern of injuries suggests that the attacker has a unique style of charging in from the right side. All of these points to only one person, his young son, Ruby.

Fear washes over Norman's face as the picture falls into place. Hyperbeam, irontail and confusion are the signature attacks of Ruby's Poochyena, Skitty and Ralts. Attacking from the right is a style the boy developed from the teachings he gave him. If any other young child comes across a wild Salamence, he or she would certainly flee right away. But Ruby is a prideful kid who will not give up any chances to battle, and battled he did. Unfortunately, it is clear that Ruby failed to knock out or capture the Salamence, and only managed to overpower it, causing the dragon to go beserk, and barge into the research tower.

Meanwhile, at the arena building nearby, the Chairman of the Pokemon Association and Wattson are still waiting for Norman to show up for the selection test. The Chairman starts to get impatient, and Wattson wonders what could be keeping their candidate. The Chairman grunts that a few minutes more is all he will wait, but just then, one of the staff rushes in to holler that something terrible has happened at the research tower.

The Chairman and Wattson quickly dash out without hesitation, and are horrified by the sight of the half collapsed building in front of them. The Chairman begins to fume with rage when he learns that their special Pokémon has escaped, and demands to know who is responsible. Behind him, Norman slowly walks up with a solemn look, and admits being at fault for the incident.

A few days later, Norman stands in front of the Pokemon Association panel to hear his punishment. The Chairman says he frankly doesn't have a clear idea of what happened at the research tower since Norman is so unwilling to reveal it, but one thing for sure is that the Pokémon which escaped is an important asset to the association. Thus, he is taking away Norman's right from sitting for any gymleader selection tests in the following 5 years, and within that time, Norman must locate the escaped Pokémon.

Norman accepts all the conditions without a single complaint, and only wishes to know why the association is monitoring and studying the serpentine Pokémon. However, the Chairman snickers that it is none of his business, and puts on a look of disdain. Norman is clearly outraged by the Chairman's attitude, but holds his tongue and simply shares a hostile glare with the other man.

Soon, it comes to the day that Norman must depart on his own to search for the escaped Pokémon. His wife couldn't stop crying as he apologizes to her for not being able to stay with her and Ruby for a good while. Struggling to hold back her tears, the young woman bends down to tell Ruby to say goodbye and wish his father a good journey, but the boy simply stares at Norman with an upset and baffled look.

Ruby slowly walks over to his father, and wonders if he has decided to stop teaching him about Pokémon battling. Norman hesitates for a while, and says one's training is a continuous process. One should never give up midway, but should aim for the extreme. However, from now on, he cannot teach Ruby anymore. Ruby must learn and discover his own strength, because only then will he reach his full potential, and achieve the state of being truly powerful.

All this is clearly too hard for Ruby to understand, and the young boy throws himself at his father's legs, pleading him to take him along. Despite the agony inside, Norman knows it is not an option to him, and sends out his Slaking to carry Ruby away from him. Watching Norman turn and walk away, Ruby thrashes around, trying to get free, but to no avail. He yells that he really likes learning about Pokémon battling from his father, and that he can only be strong under his teachings.

But regardless of how many times Ruby calls out to him, Norman remains stone-hearted and keeps on walking. He then sends out his Flygon to climb on it, and lifts off into the skies. Ruby finally breaks into tears, and pleads his father not to abandon him, but Norman is already too far away to hear him.

And so the years go by. Weathering through cold winters and hot summers, Norman trails after the elusive serpentine Pokémon, and eventually discovers its habitat at the very top of the Sky Pillar…

Ruby breaks into a brawl as tears tumble down his cheeks. Because of him, Norman was stripped of the chance to become a gymleader for 5 years, something he knows that Norman has dreamt of for a long time. Because of him, Norman was forced to chase after Rayquaza and sacrifice the time he could spend with his family while being accused for that. Because of him, Norman took up the mission to awaken Rayquaza, a task which has obviously taken an unimaginable toll on his body. Ruby shakes his father by the shoulders, and questions hysterically why he has to place the responsibility on his own shoulders.

Just then, Courtney's fire lighter drops onto the ground and ignites a flame itself, and Ruby hears the answer to his question via Courtney's voice. Courtney knew that Ruby would be asking why Norman did all that for him, and says it is the same reason Ruby locked up Sapphire in the air-car, that when it comes to the welfare of one's most important person, one would do anything, even though it might be a painful task, even though their actions may not be understood by others, even though it might be a matter of life or death.

Before Ruby could say another word, Norman closes his eyes and becomes motionless. Ruby tries to wake him but to no avail, and finally lets out a deafening yell of agony while clutching his father tight. Behind him, something blasts out from the collapsed Cave of Origin, and sends the rubbles flying everywhere.

On the Mirage Island, Juan, Tate and Liza stand side by side, and watch all the happenings at Sootopolis via the aqua screen created by Kingdra. Tate remarks that everything seems to be over now, as Groudon and Kyogre have both returned to their respective places. Liza agrees that while she was shocked when Ruby locked Sapphire into the air-car, she's glad that the titans' clash was finally put to an end with the combined efforts of Ruby and Rayquaza.

Liza states that the prediction Juan had didn't come to pass afterall, and Juan wonders what she is talking about. Tate explains that it is the premonition Juan kept having, about Ruby and Sapphire engaging in a destiny's face off with Groudon and Kyogre, and says it doesn't seem to be necessary now.

However, Juan isn't so sure. He reveals that the image he has been seeing in his head actually involved Ruby and Sapphire fighting against two powerful forces only, and did not reveal the identity of those forces. All along, he has been assuming them to be Groudon and Kyogre, but he has a feeling that he might have been mistaken all this time. Tate and Liza gasp at Juan's words, and realize that the two deadly forces waiting for Ruby and Sapphire might have been something else afterall.

Back at Sootopolis, Plusle and Minun are getting unsettled inside the air-car. The two keep shooting electricity out from their cheeks, and Sapphire couldn't understand what they are trying to do, as the ancient titans have already gone. She notices that they are directing their bolts towards the direction of the ascended ground, and gets the feeling that something else is still up there.

On the ascended ground, Archie and Maxie climb out from the rubbles of the Cave of Origin, while their Tentacruel and Houndoom stand in combative stances. Ruby gasps at the sudden appearance of the two evil team leaders, and realizes that after they were freed from the Red and Blue Orbs' constraints, they have been hiding inside the Cave of Origin the whole time the battle was going on.

Maxie grins that it is a clever reasoning, and Archie states that they will not forgive lower class trainers like him for getting into their way and challenging their authority. He hollers that interferers as such deserve to die over and over again, and claims that it is time for punishment. With that, Tentacruel shoots out its multiple tentacles to lift Ruby off the ground, and begins to strangle him…

Thanks To Coronis For Writing this for us