In the mountainous area near the Dark Cave, Silver stays airborne on Honchkrow while his Weavile hops between the boulders below with a pouch strapped across its shoulder. A wild Sneasel who is riding on the back of another Weavile approaches Silver's Weavile, and hands to it the Plate that it has found within the cave. Silver's Weavile thanks it with a wave of its claw, and places the rectangular item into the pouch, which already contains half a dozen of Plates. Later, outside the open seas of Olivine, another wild Weavile bounces up into the air on a Mantyke, and gives Silver the Plate that it has located and obtained. The red-haired boy winks to show his gratitude, and continues to head north on Honchkrow.

With the help of Morty's distant vision, Silver has learnt of the location of the remaining 13 Plates. Using Weavile's unique way of communication by carving on trees, they have managed to quickly spread the details regarding their quest to other Sneasels and Weaviles across the region, who have responded one after another with either the actual Plate or information pertaining to the item's exact whereabouts. From the green meadows of the Moomoo Farm to the chilly caverns of the Ice Path, to the decks of the sailing liner S.S. Aqua, Silver has received help in every step of his way, and finally finds himself at the western cave entrance of Mt. Mortar near Ecruteak, where a wild Weavile presents to him the last and sixteenth Plate hidden within the mountain.

Silver carefully lays the 16 different coloured Plates on the ground in front of him, and could tell from their shades how they correspond to the 16 Pokemon types with the exception of Normal: Fire, Water, Grass, Electric, Ice, Fighting, Poison, Ground, Flying, Bug, Rock, Ghost, Dragon, Dark, Steel and Psychic. Grateful that he has finally collected the full set, the boy gets ready to join Gold, who if he recalls correctly, is currently at the Ruins of Alph, which is located to the southeastern direction from Ecruteak.

Clutching onto the strong feet of Honchkrow, Silver once again lifts himself into mid-air, but just as they fly over the woods that are on the southern borders of Ecruteak, Honchkrow quacks and flaps its wings vigorously to warn Silver of something below. Silver gazes down to where the black crow is gesturing towards, and gasps in shock when he sees Crys and her Xatu lying battered on one of the tree branches.

The red-haired boy hops down and hurries over to check on the girl, who slowly opens up her eyes and responds with a weak tone. Crys sees the multiple injuries Silver has sustained on his face and body, and knows that they must have been inflicted when Arceus destroyed the Ecruteak Gym with its powerful blast. She feels sorry for causing unnecessary harm to Silver, for such a thing could have been prevented if she successfully captured the Pokemon in the first place.

Silver's eyes widen in astonishment when he realizes that the four-legged creature that attacked them was no other than Arceus, and finally puts to place this final keyword that Lance has mentioned in his phone call with Clair. Crys states that she has actually managed to trap Arceus in a Pokeball temporarily, during which she could feel it opening up its heart towards her, even just slightly. Yet, she still failed to catch it at the end, and when she attempted to give chase on Tupeon after it flew away, the deity-like creature attacked her and knocked her off the air.

Crys feels responsible for the Gym's destruction and Silver's injuries, and blames herself for not living up to the name of a Capture Specialist. However, Silver assures her that she has already done her best, and remarks that because of her, he has successfully collected all the Plates. Crys bolts in surprise to hear that, and Silver digs out the 16 Plates in his pocket to show her, grinning that he would not have been able to reach Morty and find out about their locations if Crys had not thrown herself forward to keep Team Rocket at bay when they were ambushed on Route 38.

Silver then offers his hand to help Crys climb onto the back of Honchkrow, and tells her not to worry about Arceus. Crys wonders what makes him so sure, and Silver says with confidence that it is because Gold is already battling it. With that, Silver grabs the feet of Honchkrow, and the black bird resumes its flight towards the Ruins of Alph with the two Pokedex Holders.

Meanwhile, at the Ruins of Alph, the Four Generals of Team Rocket stand on a cliff and keep their watchful eyes on Arceus. Proton uses his computer to analyze the status of the alpha Pokemon, and states that the territory Arceus created around itself is a mysterious zone that could overlap the Ruins of Alph with other dimensions. Archer believes that this zone must act like the door to alternate worlds, and will definitely lead them to the entrance of the Sinjoh Ruins.

As soon as he says that, Arceus raises its head towards the sky, and Ariana gasps that its mysterious territory is starting to sink into the ground. Archer wants to know how they could penetrate into the zone, and Proton assures him that he already has it all figured out. Archer, Ariana, Proton and Petrel go airborne on Crobat, Murkrow, Zubat and Golbat respectively, and start diving towards the energy field that surrounds Arceus. Just then, Petrel notices a Honchkrow flying in from a distance, and spots that the red-haired boy and capture girl have also arrived.

High up in the air, Crys and Silver could see that Gold is having a hard time fighting Arceus, and wonder what the energy zone around them is. Silver notices the dwindling size of the zone, and cries that they must take a chance to try barging in, even if it carries the risk of hurting themselves. Crys agrees fully, and clutches tight onto Honchkrow and they lunge towards Arceus's mysterious territory. At that moment, the Plates in Silver's pocket give off an intense glow, and catch the attention of Arceus, who is just about to crush Gold with its hooves. A resonance echoes between Arceus and the Plates, and Silver and Crys are quickly sucked into the energy zone with little resistance.

Gold is glad that his companions have arrived after all, and in that instant, Arceus rears itself up to turn the mysterious zone into a blinding globe of light, creating a multi-directional gravitational force that rips through the bodies of Gold, Silver, Crys and the Four Generals…

Later, as Gold's vision gradually returns to normal, he is astonished to see snow falling around him. A gush of chilly air seeps beneath his clothes, and he couldn't help but take a big sneeze. Trembling from the cold, Gold looks around, wondering where he is, and sees that Silver and Crys are actually right beside to him. The two are glad that Gold survived his fight with Arceus, and Gold greets them with a cheeky tone, grinning that they seemed to have gotten away just fine, although it felt a little bumpy.

The three Pokedex Holders then get back on their feet, and start to take a serious scrutiny at their surroundings. Apparently, they have arrived at the entrance of an ancient temple sitting in the middle of a snowy region. Silver wonders where exactly there are, and Crys says it appears to be some kind of ruins again. The three scan the area for traces of Arceus, but the deity-like Pokemon is nowhere to be found.

Gold hesitates for a moment, and remarks that he could have been mistaken, but back when Silver and Crys broke into Arceus's mysterious zone, he felt an abrupt change in the creature's emotions, almost as if something has quickly drawn its attention, even halting it in its attack on him. Upon hearing Gold's words, Silver also recalls a weird warmth sensation on his waist the moment he and Crys entered the zone. He reaches into his pocket, and realizes that the heat very likely came from the pouch containing the Plates.

Opening up the pouch, Silver shows Gold and Crys the mystical items, and Crys wonders what could have caused them to heat up. Silver states that in Morty's vision, the Ecruteak Gymleader saw an image of the 16 Plates overlapping with the silhouette of Arceus. He has pondered on the thought for a while now, and believes that the Plates are probably Arceus's unique hold items. In fact, given their powers, they might as well have originally been parts of the deity-like Pokemon's body.

Gold remarks that he cannot tell if Silver's postulation is correct, but if these Plates mean something to Arceus, they could perhaps use them to discover the reason behind the sorrow in the creature's eyes. He points to the entrance of the ancient temple, which appears to be the only way to advance from their current position, and says Arceus is probably somewhere inside the ruins. With that, the three Pokedex Holders brace themselves against the snow, and dash towards the dark opening.

As soon as they set foot into the temple, they find themselves on a corridor lined with Rhydon statues. Standing in the middle of the path ahead waiting is no other than the Team Rocket General, Archer. Crys demands to know what the guy is doing there, but the TR General ignores her question. Instead, he starts speaking of a folklore which describes a group of humans originally hailing from Sinnoh who moved to live in Johto and caused blending of the two cultures. He states that the ruins where they are now in fact resembles the place where Arceus awakens in Sinnoh, and although the temple contains elements from both regions, it is neither part of Sinnoh nor Johto, but known as the Sinjoh Ruins.

As Gold, Silver and Crys follow Archer into the interior of the ruins, they are horrified to see Arceus struggling in the middle of the room, fighting against multiple chains on its neck and limbs which are dragged along by the Pokemon of the Four Generals. Proton, holding his touch-screen computer, thanks the three young trainers for their effort, and says their pure intention in communicating with Arceus has made it opened up its heart and unlocked the path to the Sinjoh Ruins, which is apparently located in a dimension that cannot be easily seen or found.

Ariana expresses her gratitude to them as well, and Petrel demands the three to hand over their completed set of Plates as he orders his Golbat to tighten the chain on Arceus's neck. Seeing how their enemy has the alpha Pokemon in hostage, Gold tells Silver to give them the items, and Crys gasps in shock at his decision. Silver hurls the pouch of Plates towards the Generals after a moment of thought, and Archer grins that everything is ready now.

Gesturing to the Pokemon who are dragging the chains, Archer commands them to bring Arceus onto the platform in the middle of the temple, which is named the Mystri Stage…