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 chasing after 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, Gold keeps his gaze on Arceus, and calls out Aitaro, Politaro, Sutaro and Suntaro from their Pokeballs. The giant white Pokemon's eyes twinkle with an eerie light, and an energy field suddenly starts to rise from the ground to form a globe around itself and Gold. The boy bangs on the energy field to find himself trapped within what seems to be an alternate dimension, and angrily demands to know what the deity-like Pokemon is trying to do, stating that it is certainly not cool to imprison someone like that.

Remaining silent, Arceus stares down at Gold, and with a swing of its head, fires a powerful blast onto the ground, causing an explosion which throws the boy and his team off their feet. Gold rolls to a halt as he crashes against Explotaro, and catches a hint of sorrow in Arceus's gaze. In fact, it is a sentiment that he has already picked up when he first locked eyes with the deity-like Pokemon at Ecruteak City.

Gold somersaults away from Explotaro, and states that the sad look in Arceus's eyes makes him feel the need to help. However, it is clear that Arceus has no plans to volunteer its story, and Gold must use his own ways to find out the reason behind its sadness. As if to prove his point, Arceus thrusts its foreleg towards Gold, and the boy narrowly escapes the assault. Arceus then unleashes a burst of flame from the golden ring around its abdomen, and Gold grunts in frustration as he dashes back and forth to evade the attack. Taking out his Pokedex, Gold hopes to find out something about the alpha Pokemon, and reads that it is said to emerge from an egg before it shaped the world out of nothingness.

Back at the ruins chamber where Lance is, Bugsy looks out from the entrance of the stone hut, and sees that Arceus has created a special territory to surround itself and Gold. Lance ponders for a moment, and wants to know if Bugsy has visited the data museum at the basement of the Pokeathlon Dome. The Azalea Gymleader replies that he hasn't, and Lance explains that the museum actually houses the documentations on the Pokeathlon's origins.

Long ago, on an island in a distant region, a deadly epidemic has hit the residents and their Pokemon. At that time, a trainer and his team of Pokemon have set out to find a mirage Pokemon, whom they believe could teach them the way of remedy to cure the disease. Yet, in order to reach where this mirage Pokemon was, they must go through 10 different obstacles, which could not be overcome by man or Pokemon alone. Fortunately, the trainer and his Pokemon worked together in close collaboration, and managed to conquer the first obstacle with their equally determined souls. They were subsequently able to beat the obstacles one by one, and eventually inherited the healing ways from the mirage Pokemon. This trainer and his Pokemon were later revered as heroes by his people. In order to let their descendants remember the heroic act, the island residents invented sports that resembled the 10 obstacles the trainer and his Pokemon went through, which as time went on, evolved into the 10 Pokeathlon events of the present day.

Lance states that he initially thought if he managed to find a trainer who together with his Pokemon matches the qualities of this ancient hero, they could perhaps dissolve the deep grudge and disappointment that Arceus holds towards humans. That is the reason why he has chosen the Pokeathlon Dome as the venue to meet Prof. Oak's Pokedex Holder. However, it seems that even though he has found a trainer who apparently possesses the skills of this hero, the trust between this trainer and his Pokemon is still lacking.

The green jewels on Arceus's abdominal ring glow with an intense light, and without warning fire off laser-like beams to strike at Gold's Pokemon. Explotaro, Aitaro, Politaro, Suntaro, Sutaro and Togetaro lay battered on the ground, and Gold grits his teeth in frustration as he struggles to get up himself. He soon notices that Togetaro has climbed back onto its feet and is ready to attack again, and suddenly remembers what Lance said about it not fully bonding with him.

With a sigh, Gold says he has known for a long time that Togetaro is not opening its heart towards him. If that is the case, there is no way he could turn things around in this battle against Arceus, and he has no choice but to retrieve Togetaro and keep it as a backup. The little Togepi halts in its motions with an expressionless face upon hearing Gold's words, and after a moment of hesitation, sprints towards Arceus on its own will. Yet, Gold forcefully sends it back into its Pokeball despite its apparent protest, and opts to continue the fight with his other five Pokemon instead, whom he calls his main battling forces.

The boy orders a simultaneous Double Hit from Aitaro, Solarbeam from Suntaro, Blast Burn from Explotaro, Rock Tomb from Sutaro, and Bounce from Politaro. However, Arceus throws its forelegs forward, and smacks hard on the five Pokemon with its golden hooves, knocking every one of them down. He then delivers a kick on Gold, and sends the boy crashing against the ground.

Togetaro's Pokeball rolls off from Gold's hand, and the little Togepi fights to spin the switch towards the floor, tactfully activating it and releasing itself out. Wearing a determined look, it leaps towards Arceus, and hops up along its massive body until it manages to jump right above its head to prepare a strike down. Unfortunately, the alpha Pokemon swings its head around, and easily swipes Togetaro off with its pointed mane. Togetaro tumbles backwards as it hits the rocky floor, but quickly gets back up again, and charges forward for another attack. Gold calls it a fool, and says it could not win this way, but Togetaro seems oblivious to the words, and keeps advancing until Arceus delivers another blast to shoot it down.

Crawling over to Togetaro, Gold relents that perhaps as Lance predicted, Arceus is far too strong for them to do anything for it. He tries to grasp Togetaro by its little hand, but Togetaro whacks him off, and turns to make a face by sticking out its tongue. The mischievous look instantly reminds Gold of what DJ Mary said about him and Togetaro knowing and trusting each other a lot. At that time, he took the compliment with grace and even bragged about personally hatching Togetaro from its egg. He even said at some point that he could confidently bestow his trust in its powers, but in reality, this seems quite far from the truth.

Thinking back, in every major battle he has participated in so far, Togetaro has always played the role of a backup. In his showdown against the Mask Of Ice, he called his team of six his full team of entrusted partners, but Togetaro was left out of the picture. Even now, while confronting Arceus, he also treats it inferior to his other Pokemon, and refuses to let it be part of the main team.

Togetaro once again jumps forward in an attempt to attack Arceus, but the deity-like creature wastes no effort in swatting it down, and the little Togepi finally lays exhausted on the ground. Gold slowly moves over to kneel next to Togetaro, and says it really seemed ridiculous of him to accuse it for not opening up its heart towards him. Obviously, he is the one who hasn't opened up his heart towards Togetaro, and he should know better than anyone how it feels to constantly be in the position of a replacement.

Gold grins that he will not hide Togetaro from the spotlight anymore, and says he now wants it to help him defeat Arceus. Hearing the words, Togetaro climbs back onto its feet despite its fatigue, and dashes forward as Gold lets out a holler and orders a Double-edge attack. A glow gradually envelops the body of the little Togepi as it advances towards Arceus, and in a blinding flash, it evolves into a Togetic. The Shiny Stone it holds glitters in another shower of light, and to Gold's shock, Togetaro further evolves into a Togekiss, a split second right before it lands the blow on Arceus.

Alas, the attack fails to cause any substantial damage to the alpha Pokemon and Togetaro tumbles back onto the ground. However, Gold notices a sudden shift in Arceus's emotions, and the deity-like creature gradually spins towards the other direction while keeping its gaze on him through the corner of its eyes. Energy starts to radiate out from its body, and without warning, it resumes its attack on Gold again.

Standing on a nearby cliff that overlooks the ruins, the Four Generals of Team Rocket 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…