High up above the open seas, Mega Latios dashes across the sky in its 'Soar' mode, and suddenly senses a tear drop on its back. Apparently, Ruby has cried without himself knowing it, and the boy breaks into a little laugh as he becomes aware it, wondering why he is still weeping after having ventilated his emotions. He wipes his tears off with a handkerchief, and Latios muses to itself that humans are really mysterious beings, changing so drastically within such a short period of time. It recalls meeting Ruby the first time at the Battle Frontier, and feels that while he is basically still the same person, there are also differences then and now. The psychic dragon believes that it is the reason why it managed to Mega Evolve successfully, and knows that Ruby is the human it is meant to bond with at this point of time.

Mega Latios asks if they should just head to Sea Mauville directly, and Ruby replies with a nod. He states that he wishes to apologize to Sapphire, and also thank Emerald who has been helping him keep the secret. Afterwards, he shall ask for their help in finding Rayquaza, since they have little time left and there are only a handful of hints on Rayquaza's whereabouts. Latios wonders what hints Ruby is talking about, and the boy explains that he has four places in mind. First, the Sky Pillar, where the dragon slumbered 4 years ago, which they have already finished investigating. Second, the Mossdeep Space Center, which should hold the records that documented his father's search for Rayquaza. Third, the Draconids' village, which location is unknown but he believes can be worked out from the wild habitat data he collected with Sapphire. Last but not least, the Pokemon Association's research building, where he set Rayquaza free 9 years ago. Ruby winces in pain as he suddenly feels a tug at his heart, and Latios gets worried. Ruby assures it that he is alright, and tells it to just focus on its flight.

Meanwhile, at Sea Mauville, the chest piece of Ruby's recently evolved Gardevoir, Rara, flashes intensely, and Sapphire realizes that it has picked up its trainer's emotions. She wears a look of concern, and wonders where the boy is. At her feet, Plusle and Minun cling onto her tightly with anguished expressions, and Emerald can see that they are both frightened. Sapphire states that she feels horrified herself, and steals another look at Chic and Sceptile, who writhe in agony with blank looks on their faces as their bioenergy gets extracted by the Absorber.

Unable to keep her silence any further, Sapphire confronts Steven, and wants to know what exactly is going on. She fails to understand why they have undergone special training to polish their battle skills when what is taking place to Chic and Sceptile's bodies will clearly render them unable to fight very soon. She also finds the Dimension Shifter device very disconcerting, and requests an explanation on its purpose. Steven gets a little uneasy at her query, and ponders on what to say. Before he could give a reply however, a female voice comes on and states that Sapphire will never get her answer since Devon is a heartless corporation that exploits humans and Pokemon to the end just to fulfill its own goal.

Sapphire quickly looks up to the second floor, and sees that the speaker is a woman with short black hair wearing a cape who is accompanied by a Whismur. Behind her, Team Magma and Team Aqua Grunts stand in a line, but instead of fighting each other like they did 4 years ago, they appear to be working in collaboration. Sapphire is astonished by what she sees, and demands to know who the woman is. The woman cocks her head in contemplation, and says it is a surprisingly difficult question. She sighs that she couldn't become who she was supposed to be, and doesn't know what it makes her now. She then laughs that she is just kidding, and says it is not the time for introspection and soul searching. She introduces herself as Zinnia, one of the Draconids, and her answer causes Steven and Joseph Stone to gasp in shock. Emerald finds the name extremely familiar, and suddenly recalls that she was the woman who infiltrated Team Magma and led them to awaken Groudon 4 years ago. Sapphire bolts at the revelation, and Zinnia is impressed that Emerald knows so much. She giggles that Team Magma was not the only organization she infiltrated however, and says she also disguised herself as a Team Aqua Grunt afterwards, and even witnessed the awakening of Kyogre.

Steven demands to know if she is the one who sent them the threat letter, and Zinnia is offended by his choice of words. She barks that they only perceive it as a threat because of all the filthy things they do, and decides to fulfill the promise stated in the letter since Devon didn't take their advice to stop using the Infinity Energy. Reaching for a Pokeball, Zinnia sends out her Goodra, and orders a Sludge Wave. The attack hits the Stones directly, and Steven tries his best to shield his father. Zinnia gestures to the Magma and Aqua Grunts behind her, and says they must use all their might to put a stop to Devon's evil deeds. The Grunts respond with a roar, and proceed to call forward a Numel, Carvanha, Koffing and Grimer to attack.

Drake, Ultima and Mr. Briney quickly defend with Shelgon, Dragonite and Pelipper, and wonder why the Magma and Aqua Grunts have come. Zinnia explains that these are the people whom she let in on the secret of their planet's impending crisis when she infiltrated the organizations, and says they are all fighters with a conscience who are willing to overlook their team differences to help her protect the planet from Devon's evil hands. A vigorous battle soon breaks out, and while Pelipper and Shelgon deal with the Grunts' Pokemon, Dragonite takes on Zinnia's Goodra.

Joseph Stone cries that the fighting must stop or it may damage the Absorber, which will cause all the bioenergy extracted from Mega Blaziken and Mega Sceptile to go waste. Zinnia snickers that her target isn't the Absorber but rather the Dimensional Shifter being charged on top, and Sapphire discovers with a start that the woman's Whismur has secretly approached the device and pulled it off from the circuit. Zinnia compliments Aster for its work, and tells it to come back down with caution. However, before the Whismur could return to its trainer, it is ambushed by Plusle and Minun, who snatch the device and hand it over to Sapphire instead.

Zinnia teases that Sapphire doesn't even know she is holding, and the girl makes no attempt to hide the fact. She genuinely wishes to understand what the device is and what exactly they have been asked to do, and Zinnia decides that she deserves the truth. Joseph Stone quickly interrupts and tells Sapphire not to listen to Zinnia, but Zinnia pays no heed to the man, and reveals that the Dimensional Shifter is a machine that can create a warp hole. By generating a portal in space, the device is meant to warp away the giant asteroid that is about to collide with their planet. As soon as Zinnia mentions the asteroid, Joseph Stone drops his head in silence, and Sapphire's eyes widen in bewilderment. Zinnia notices her unusual response, and realizes that she doesn't know anything about it. She questions how Sapphire can work with Devon without knowledge of the situation, and Sapphire quickly turns to the others for answers. To her dismay, Steven, Mr. Briney, Ultima and Drake all avert their gazes from her, and even Emerald wears an uneasy look on his face.

Sapphire refuses to believe that everyone but her knows about the asteroid, and wonders if Ruby is aware of it as well. Zinnia replies that the arrogant boy surely does, and her response makes Sapphire realize that the two have apparently met. In the next instant, a million thoughts race through her head, and she finds it hard to accept that she is once again the only one left out, once again being dumped aside by Ruby when he met this woman, once again seeing history repeat itself and having everyone keep a secret from her. Fuming with rage, Sapphire raises her voice and demands to know where Zinnia met Ruby. However, before she could finish her sentence, she suddenly loses her voice and fails to make a sound. Without warning, Zinnia lashes out to grasp her wrist, and Sapphire quickly somersaults backwards before the woman could snatch away the Dimensional Shifter. She begins to flee to the other side of the room, and Zinnia orders the Grunts to chase her down and destroy the device.

Zinnia turns her attention back to the battle, and sighs that she was merely a few inches from getting her hands on the Dimensional Shifter. However, she thinks it is alright since she has at least managed to stop its energy filling. More importantly, she has managed to seize Sapphire's Mega Bracelet, which earns her a Keystone. She glances over to the Mega Stickpin on Steven's pocket, and decides to make it her next target.

While the Grunts scout for Sapphire on the ground floor, the girl climbs onto a steam pipe to keep herself hidden. She is soon approached by Emerald, who has found a hiding place on the second floor, but she angrily swats his hand away, and feels upset that he is lying to her as well. Yet, as she could not speak, Emerald doesn't understand what she is trying to say, though he can understand her fury. He tries his best to pacify her, and apologizes for keeping a secret from her. He promises that Ruby will explain everything when he returns, and urges her to find shelter before the Grunts discover her. Unfortunately, an Aqua Grunt eventually spots them and alerts the others of their location. Emerald tells Sapphire to run, and quickly sends out Sudowoodo and Dusclops to fight. At that moment, unbeknownst to everyone, the mysterious humanoid Pokemon Emerald recently battled on deck materializes out of nowhere and sneaks up on Sapphire. It stealthily expands the golden ring it holds, and catches the girl by surprise as it sends her through the portal within.

Meanwhile, Steven has sent out his Metagross and Mega Evolved it to fight Zinnia's Goodra. The gooey dragon strikes out with its antennae, and Mega Metagross promptly defends with its touch claws. Joseph Stone demands to know why Zinnia is interfering with their plan, and knows she must be aware of the crisis their planet is facing. He hollers that they have created the Dimensional Shifter for the purpose of saving their planet, and says it is a science technology which they have poured all of their hearts and souls into. He cries that it is the only hope for humans, but Zinnia disagrees. She barks that they are simply repeating the same mistake humans made thousands of years ago, and points out that the number of lives cost back then was beyond imaginable. She finds it unforgiveable that Devon is proceeding with acts that they well know would corrode not only humans and Pokemon but also the water, the land and the air, and scorns at their flawed thinking that no consequence is too hard to bear as long as the asteroid does not collide with their planet.

Mumu feels troubled as Zinnia and Steven bring their battle onto the deck, and suddenly spots a silhouette approaching Sea Mauville from above. Its face beams with recognition as it notices the person riding on the airplane-shaped Pokemon, and quickly runs over to the bowsprit in expectation.

Goodra breathes out a blast of fire, and Mega Metagross struggles hard to shield its trainer as it fends off the flames. In the next instant, a powerful hand grabs Goodra by the face to stop its attack, and subsequently hurls it over, causing it to crash along with Zinnia. Mega Metagross takes the chance to strike out, but its blow is blocked by the same hand. Steven gasps in surprise, and sees that Ruby has arrived and also Mega Evolved his Swampert. The boy stands between the two parties, and urges them to stop their pointless fight. His remark astonishes everyone, and Zinnia thinks he must be out of his mind. She tells him to get out of his way, and gets Goodra to spit out its flames once more, which Mumu manages to withstand. Ruby grunts that it isn't easy to convince them after all, and knows he must first pull Sapphire and Emerald out from Devon's plan. However, he soon realizes that Sapphire is nowhere to be found, and wonders where she has gone.

Out on sea Route 131, another meteorite plummets into the sea from the sky and creates a gigantic splash. Standing on a rocky islet nearby, Gabby holds onto Absol as she asks if Ty managed to film it, and the drenched cameraman replies that he has got it all on tape. Ever since they set out from Slateport with Absol, this is already the sixth landing they witnessed: the first one in Ever Grande's nearby sea, the second on sea Route 132 near Pacifidlog, the third on sea Route 127, the fourth on sea Route 124 near the coastline of Lilycove, the fifth on sea Route 130, and the sixth on sea Route 131 where they currently are. Gabby points out that all sites are within the proximity of Sootopolis City, and Ty thinks it is fortunate that all meteorites have so far landed directly into the sea without causing any casualties or damage to the towns and boats. Gabby wants to know if this is the disaster Absol wishes to show them, and the white creature nods in silence. Gabby believes that they will have to depend on themselves for the next step of investigation, and decides to retreat for now.

Later, back at Hoenn TV's Slateport branch, Ty finishes uploading all his recordings onto the computer, and wonders what to do with them. Gabby wagers that they should pay a visit to the Mossdeep Space Center since they are dealing with objects from space after all, and is determined to get to the bottom of this in order to make a good and accurate story. Until they do, however, she thinks they should put the footage away safely, since it may cause unnecessary panic to the entire Hoenn if it leaks out. Ty agrees, and the two decide to take a short snap before they set out for Mossdeep. As Gabby and Ty leave the room, a man in glasses who is accompanied by a Spinda sneaks up on Ty's computer, and smirks that he may have stumbled upon some invaluable data…