At the Ilex Forest, the Team Rocket Elite Trio, Ken, Al and Harry, wander through the woods and find that the place still feels like a maze even after having patrolled the area for so long. Ken remarks that they really shouldn't complain, since they received the order directly from that person. Al agrees, and Harry sighs that he has missed this feeling of working for their true leader. He reveals that it completely thrilled him when the man just appeared all of a sudden, and ordered them to eliminate all shady intruders at the Ilex Forest. He believes that with the man back, they will not have to listen to the Four Generals anymore. Ken and Al agree, and vow to give their best and fulfill this mission the man bestowed upon them.

Suddenly, something lands in the bushes behind them, and the three quickly bolt to their feet. Determined to rid all shady intruders, they send out their Hypno, Mime Jr. and Skorupi, and soon see that they are facing a yellow creature that is sparkling with electricity.

Back at the Sinjoh Ruins, Gold, Silver and Crys gasp with disbelief at the unexpected arrival of the three men, Lance, Pryce, and Giovanni. Archer beams with excitement at the sight of his former leader, and as he blurts out the man's name, Gold and Crys put on shocked expressions and turn to Silver, who acknowledges the fact that the man is his very own father, also the true boss of Team Rocket whom he has been searching for all this time.

However, what stunned Gold more is the presence of Pryce, the former Mahogany Gymleader, who should have vanished into the voids of time long ago, but is now sitting in his wheelchair again with his Swinub on his lap. Pryce puts on a grin, and expresses his understanding of Gold's astonishment. Lance states that the three of them have all tried to take over the world at some point, which makes them the villains. Moreover, they are linked to each other individually due to past karma, which is beyond complicated. Yet, all the explanations will have to wait, because their top priority now is to prevent the three newly created legendaries from having a full force clash with each another.

On the Mystri Stage, Dialga and Palkia stare down at Giratina, while the serpentine creature does the same. Lance points out that although the three have just been born, they apparently retain memories of their ancient past. Dialga and Palkia are clearly antagonistic towards Giratina, who displays similar hostility towards the two. Pryce states that it is only logical, since long ago, Dialga and Palkia banished Giratina into the other side of the world after it wrecked havoc in the real world. The alertness and sense of duty of Dialga and Palkia, as well as the pent-up grudge of Giratina have obviously rooted deep into the body and minds of the three.

Pryce turns to Archer, and comments that it is a foolish act to try to exert control over Dialga, Palkia and Giratina without knowing the sentiment shared among them. Archer is ticked off that the old man states facts as if he has seen it personally, and hisses that it is all from tales and he would not have known what really happened. However, Pryce reveals that he has indeed seen the happenings with his very own eyes within the voids of time, and his words cause Gold to widen his eyes in astonishment.

Pryce then tells his Swinub to get ready, and says they only have to catch the dragon's attention without needing to start a direct conflict. Swinub complies by sending out a blast of snow from its snout onto the back of Dialga, and the temporal dragon quickly turns around to glare at its attacker. It raises its head to let out a high-pitched roar, and Pryce's actions in the recent few seconds suddenly get reversed and undone. Yet, the former Mahogany Gymleader, who easily recognizes the attack as Roar of Time, is barely fazed, and grins that the move will not cause much harm to someone who has attempted to control time.

While Pryce keeps Dialga occupied, Lance decides to take on the dragon which governs space, and orders a Hyper Beam from his Dragonite. Palkia raises its arm to deliver a Spacial Rend, which creates a dimensional tear and warps the attack to the outsides of the Sinjoh Ruins chamber. However, as Dragonite is capable of controlling the direction of its Hyper Beam, it bends the attack at angles to direct it back inside the chamber, and hits Palkia from behind, catching the spatial dragon with total surprise.

Meanwhile, Giovanni orders Silver's Ursaring forward, and prepares to fight Giratina, the dragon which governs antimatter. Archer feels devastated by Giovanni's actions, and fails to understand why he is hurting the newly born legendary Pokemon he worked so hard to bring to existence. Running towards the man with a look of despair, he begs him to stop, but Giovanni rams his hat hard into Archer's face to quiet him. He then addresses Ariana, Proton and Petrel, and tells them to simply stay put for now, as they shall receive their appropriate punishments afterwards. Ursaring throws itself towards the serpentine creature as it dives forward, and delivers a series of brutal slashes to smack it down. Giratina wraps its tentacles around the giant bear to restrain it, but Ursaring flings its arms around the dragon's neck to choke it and forces it release its grip.

Gold, Silver and Crys watch with amazement and cannot believe how quickly and easily the three men subdued the legendary Pokemon. Pryce states that they do not have another choice, because if they do not interfere with the three Pokemon, they will not be able to return safely to where they came from in the original world. Crys gets confused by what Pryce says, and the old man tells them to check the map on their Pokedexes. The Johto Dex Holders do as they are told, and are shocked to see that their current location falls outside the Johto region, although they came to the Sinjoh Ruins via the Ruins of Alph.

Pryce explains that the Sinjoh Ruins' location will not show up on the map, because it is an area that exists in an alternate dimension. To put it in another way, the ruins lie in a special realm which links up Johto with a faraway region, Sinnoh. That said, it is an extremely unstable area, and if the three legendary dragons shall start a full force clash there, the special realm will fall apart. As an inevitable consequence, both Johto and Sinnoh will also fall apart.

Pryce then corrects himself, and says the two regions did fall apart, because he witnessed it in the voids of time. Gold, Silver and Crys gasp in horror as Pryce explains how Johto and Sinnoh ended up in total annihilation, and the old man remarks that the dragons' clash must be prevented at all means, which is in fact the reason why he was brought back. Gold is astonished to hear the passiveness in Pryce's return, and wonders who it was that brought him back. Pryce states that Gold himself has come into contact with this being before, and the boy bolts with realization that the old man is talking about the time travel Pokemon, Celebi…