Sitting on his Regirock, the Pyramid King Brandon receives a call on his PokeNav Plus, and is pleasantly surprised to find it coming from his close acquaintance, Palmer. He greets the man warmly, and wonders if he is now in Johto or Sinnoh. Palmer replies that he has returned to Sinnoh to spend time with his family, something which he has not done for a long time, and says he is currently watching a comedian show videotaped from Johto television with his son, who is a big fan of stand-up comedies. Yet, he couldn't help but feel concerned, and wonders if there is really nothing he could do about the present situation. Hearing that, Brandon lets out a sigh, and says being with his family is probably his highest priority right now. Palmer falls silent at the remark, just as his young son asks to go out with his companion to practice Manzai. Palmer promptly stops them, and suggests they stay indoors for the coming two days, which leads to much protest from the two young boys.

Palmer wants to know how things are going on Brandon's side, and the Pyramid King reveals that he and his comrades are currently near the crash site of the Mossdeep Rocket. He is sure that Palmer must have already learnt of the Rocket's failure to launch into space, but when they arrived to survey the area, they actually found a gang of suspicious people lurking around. Naturally, they confronted these people dressed in red and blue suits, and seized them along with their Camerupt and Sharpedo-shaped submarines.

It turns out that these suspicious people Brandon referred to are no other than Courtney, Tabitha, Shelly and Matt, the Admins of the Neo Team Magma and Aqua. Although the four did attempt to put up a fight, they were clearly no match for the Hoenn Frontier Brains, who quickly overpowered them and even forced an explanation out of their mouths. To be fair, it was Tabitha who failed to keep his silence, and Shelly, who is held immobile by Anabel's Raikou, scoffs at him for buckling under pressure so easily. The chubby man cries that he has low tolerance for pain, and winces in agony as Noland's Mawile clamps him between its jaw-shaped horns.

Greta grabs Courtney by the collar and demands to know where this person called Zinnia is, but Courtney keeps her expressionless face and simply giggles that she doesn't know. Matt, who is hung upside-down on Lucy's Seviper, swears that they really have no idea, and at that moment, Anabel hears her name called from afar. She turns to Lucy to ask if it was her who spoke, but the Pike Queen shakes her head in response. The voice calls out again, telling Anabel to look up, and the Salon Maiden soon discovers in astonishment that Emerald is waving to her through a mysterious opening in the sky which is bound by a golden ring. Bewildered, Anabel wonders how it is possible, but Emerald suggests they leave the details to later and wants to know if Sapphire is with them. Noland recalls that the girl is one of the Pokedex Holders, but Tucker replies that they haven't seen her. Then, just as abruptly as he entered the scene, Emerald vanishes with the golden ring into thin air after a brief acknowledgment of their answer, leaving the Brains feeling lost and confused.

Back at the Draconids' Village, Emerald states that Sapphire isn't at the Rocket's crash site, and thinks they should try the Mossdeep Space Center next. He gestures to Hoopa again, and focuses his mind on Sapphire and the Space Center as the little genie channels these thoughts through its golden ring to summon a new location. Soon, a new scene manifests within the ring, and Tomatoma wonders if they have succeeded. However, it appears that they are looking at some kind of cave, which has been elaborately decorated with carpets, posters and dolls. In the middle of the room lies a giant tent, and a young man with a goatee crouches at its opening, seemingly tending to someone resting inside.

Waking up from her coma, Sapphire sits up and finds herself lying in a tent. The man with a goatee crouching beside her is glad to see her come around, and reveals that he has healed up her Tropius at the Fortree Pokemon Center. Sapphire struggles to get up, but the man tells her to take it easy as she hit the water pretty hard after all despite being protected by her Tropius. He introduces himself as Aarune, a 25 year-old hailing from Unova who is travelling across the world to spread the good word about Secret Bases. He explains that they are currently at a Super Secret Base on Route 120, which is built under his guidance by a young trainer. Earlier, this trainer wished to migrate to a new base and he was in the process of helping him when Sapphire suddenly fell from the skies. He thinks it is fortunate that they were at the scene, or she would have probably drowned.

Just then, they hear a noisy bickering, and Sapphire quickly recognizes the voice. She scurries out of the tent, and immediately sees an opening in midair which is lined by a golden ring. Inside, Emerald yells at Hoopa for messing up the destination, but Hoopa clearly thinks otherwise and strongly protests against the accusation. Luckily, Tomatoma spots Sapphire, and quickly alerts Emerald. However, before Emerald could say anything to Sapphire, a loud bang goes off at the Draconids' Village and the entire ground begins to rumble. In the next instant, Primal Groudon breaks out from the ground while Primal Kyogre leaps out from the giant lake in the middle of the room. Maxie and Archie soon show themselves, and appear to be quite pleased by the fact that the ancient titans have finally mastered the moves Precipice Blades and Origin Pulse. They wonder if they should find something to test on, and both Emerald and Tomatoma immediately put their guards on and get into combative stances. Yet, it is Hoopa who reacts most violently, as it suddenly charges towards Primal Groudon and Kyogre and starts smacking at them with its two active golden rings, the one connecting to the Secret Base and the other to Johto. Emerald hurriedly cries for Hoopa to stop, but the little genie wouldn't listen and keeps on attacking.

Meanwhile, in Johto, Norman has climbed onto the back of Rayquaza while Ruby is still in its grasp. The Petalburg Gymleader wants to know if his son is alright, and although Ruby is obviously in pain, he feigns a nod and grins that the powered up Green Orb seems to be working partially at least since the dragon hasn't crushed him into pieces yet and is even flying towards the portal as they wanted. However, as Rayquaza nears the golden ring which leads them back to the Draconids' Village, it soon spots Primal Groudon and Kyogre in battle through the opening. The scene instantly makes it go berserk, and it rears its head back as it lets out an angry roar. The motion throws Norman off its body, and Ruby cries out in horror as his father crashes onto the ground. The giant green serpent then fires a powerful beam into the golden ring's opening, which channels through the portal and exits on the other end, striking at Groudon and Kyogre while causing Hoopa to freak out.

Emerald and Tomatoma exclaim upon seeing Rayquaza, and Hoopa's eyes widen with shock as the dragon lord prepares to charge into their location via the portal. Grannie cries that they couldn't let Rayquaza through in its current state as it will surely start a battle with the other titans, and says they must find a way to quell its rage. With no time to think, Hoopa acts out of reflex and forcefully brings its two active rings together. As a result, Rayquaza traverses the two portals consecutively, and ends up on Route 120 where it blasts out from the Super Secret Base. Flabbergasted, Aarune wonders what is going on, and Sapphire gasps in recognition upon seeing the sky titan. More importantly, she spots someone being held captive in Rayquaza's claws, and with her near perfect eye sight, sees that it is no other than Ruby. Just then, the young trainer who owns the Secret Base shows himself, and voices out his own astonishment at Rayquaza's appearance.

Up in midair, Rayquaza thrashes around in fury as it tries to make sense of what is going on, and Ruby realizes that they are back in Hoenn somehow upon seeing Mt. Chimney. He tries to get the giant serpent to calm down by holding up the Green Orb, and says they should be heading to water Route 131. However, Rayquaza shoots him a glare, and without warning releases its grip to drop him from the skies. Shock and disbelief wash over Ruby as he begins to plummet. He finds it hard to accept that he is meeting his end just like that by getting thrown off from height, before he could actually save the planet and more importantly, apologize to Sapphire. Suddenly, something halts his fall, and he finds himself saved by an Altaria. A familiar voice comes on to express his relief that he made it in time, and Ruby turns around to see a boy with green hair hovering over to him on a Magnezone.

Ruby gasps in astonishment that it is his friend Wally, and the boy explains that he has decided to give chase after Rayquaza shockingly flew out from his Secret Base. Although he is simply wagering a guess, he believes that they are in need of the dragon's powers again, and it must have something to do with the giant incoming asteroid. Ruby is at a loss of words, but Wally shows his understanding, and decides to lend his strength despite knowing well that Ruby prefers to do things on his own.

Dashing towards Rayquaza on Magnezone, Wally gets the floating magnet to unleash a Discharge, and the dragon lord retaliates by firing a beam from its mouth. However, Wally adeptly steers Magnezone out of the way, and follows up with a Zap Cannon, which lands a critical hit on the giant serpent, stunning it temporarily. Wally's display of strength utterly puts Ruby in shock, and he couldn't help but notice how far his friend has gone in his pursuit of power in the past 4 years, having refreshed his team line up and all. Rayquaza pants from the paralytic effect of Magnezone's attack, and Ruby thinks with amusement that he should intervene before Wally actually takes down the titan. He quickly cuts in with Altaria to stop Wally from further attacking, and after thanking him, and says he should be able to take things from there.

Ruby holds up the Green Orb as he comes face to face with Rayquaza, and acknowledges the fact that it could also undergo Mega Evolution if his guess is correct. He believes that Rayquaza is upset because it has lost the partner it has bonded with, rendering it unable to do anything about the giant asteroid. Wearing a determined look, he offers to be the dragon lord's new partner, and thinks they would form a bond strong enough to take on the asteroid. The sky titan pauses for a moment, and just when Wally fears that it would attack again, it approaches Ruby with a calm demeanor, indicating that it has agreed to the partnership.

Ruby feels grateful that he has finally gained the trust of the dragon lord, but soon spots someone else hovering nearby. Flying on her Tropius, Troppy, it is no other than Sapphire, who is looking at Ruby with an expression of both anger and sadness. For Ruby, a million words race through his mind, but they all choke up at his throat and he could only stare at Sapphire with a helpless look…