At the Whirl Islands in the land of Johto, Silver hovers high above the chain of isles on his Murkrow, and gazes down at the numerous whirlpools that surround the area. Suddenly, Murkrow drops the Dusk Stone it is holding by accident, and Silver catches it just in time. He nags the black bird to be more careful about its hold-item, and takes a look at Sneasel in its Pokeball, who is holding the Sharp Claw, both items given to him by Blue. With her knowledge in Pokemon evolution, this sister-like figure to him has mentioned that the stone and claw have special effects on his Pokemon.

Silver soon arrives at the southernmost island, and takes a landing on a stone platform, which serves like a gate to the bowl-shaped island's entrance, with a whirlpool and a waterfall lying in between. The red-haired boy sends out his Red Gyarados to cease the whirlpool, Kingdra to split apart the waterfall, and finally Feraligatr to surf across the body of water, making his way towards the hidden room on the other side.

Passing through the stony corridor, he sends out his Sneasel to survey the area before stepping into the secret chamber, and tries to remember how long it has been since he last set foot there. He calls out to Lance, whom he is hoping to find there, but the only thing that responds is the echo of his own voice, and he figures that the man is probably not around.

Silver walks up to the throne in the center of the room, and throws out a pile of photos, all of which depict the recent incidents in Johto, including the black market selling of Slowpoke tails, the swarming of Gyaradoses at the Lake of Rage, and the mysterious radio-waves emitted from Goldenrod City. While it may seem that all these were isolated events unrelated to one other and only affected a minimal number of victims, if one pays close attention, it is clear that someone is purposely repeating these specific malicious actions, which have taken place during a previous time under the choreography of an evil organization. If anything, this string of events seems to convey one ominous message, that this evil organization which was disbanded years ago, Team Rocket, is getting revived again.

Silver holds his fist in angst, and vows to put an end to all of this if Team Rocket truly turns out to be the culprit again. He has no idea why the remnants of the organization are regrouping once more, which is why he has come to Lance, whom he thought would know of something. Yet, he has apparently returned to this old hidden home of the man at a bad time. Beckoning to Sneasel, Silver decides to leave, and turns to head for the exit.

Suddenly, a whip lashes out to wrap itself around Sneasel, and as Silver attempts to do something, the sharp horn of a Dragonair points at his back, forcing him to freeze in motion. The wielder of the whip, a young woman with blue wavy hair, shows herself with an angry look, and demands to know who Silver is. The red-haired boy recognizes the woman right away as the Blackthorn City Gymleader, Clair, and queries her reason of being there. Clair barks that she should be the one asking the question, and wants to know what the boy has done to her brother.

Silver gets baffled by her words, but after a moment of thought, rationalizes that it is Lance whom she is referring to. Clair snaps with affirmation, and states that she and Lance both hail from Blackthorn the dragon-ville and both raise dragon types. They may not be real brothers and sisters, but the bond between them is so strong that it is not for outsiders to understand. She grunts that something has definitely happened to the man, and the certainty in her tone makes Silver feel alarmed as he has not thought of that possibility. The truth is, Clair received a call from Lance earlier at her gym, but midway through their conversation, the connection was cut, and she has been unable to reach him since then. Deeply worried about the guy, she couldn't remain in Blackthorn and simply wait. Silver assures Clair that he isn't her enemy, and neither is he a foe of Lance's. He formally introduces his name to the Blackthorn Gymleader, but before he could go on, he senses a stir, and turns around to see that while he and Clair were preoccupied with each other, a pack of Koffings have secretly infiltrated the place and encircled them.

Clair lets out a gasp of astonishment, and prepares to battle. However, Silver says it wouldn't be necessary for her to get involved, which makes the young woman feel humiliated and causes her to snap in protest. Silver explains that he means no offense, but the pack's hostility is clearly directed towards him instead of her, which is why he prefers to take care of his own business. To be honest, he is unable to tell whether the creatures came to ambush him specifically or had other hidden agenda, but fighting back seems to be the only appropriate response.

With that, Silver calls forward Sneasel and sends out Feraligatr, Kingdra, Gyarados and Murkrow from their Pokeballs. Gyarados thrashes around its long body to smash against the Koffings, while Murkrow delivers a series of flaps with its powerful wings. Meanwhile, Kingdra spits out a swirling stream of water to wash up its opponents, while Sneasel claws them down one by one. Standing in the center of the room, Feraligatr takes in a deep breath, and a powerful jet of water soon explodes from its wide jaws to blast down the remaining poison floaters.

Clair and Dragonair are awe-struck at how Silver's Pokemon managed to take down such a huge number of Pokemon in just a split second, and the red-haired boy comments that it was partly thanks to the man whom Clair refers to as her brother. The Blackthorn Gymleader wonders if the move that Feraligatr just used is the ultimate water attack Hydro Cannon, and Silver responds with a nod, patting the giant alligator on its face and explaining that they once had the fateful chance to inherit it. He then takes out his new version VI Pokedex to check on its stats, which makes Clair even more surprised, realizing with a start that she is talking to a Pokedex Holder.

While Clair and Silver exchange a few words about the Pokedex, one of the Koffings slowly stirs amongst its fallen opponents, and attempts to sneak his way out, holding what appears to be a rectangular piece of item in its mouth. Thanks to his sharp senses, Silver manages to detect this stealthy move, and immediately motions to Sneasel, who leaps forward to deliver a sweep with its claws. The force from the impact allows Koffing to bounce towards the entrance's waterfall where it manages to slip away, but Silver has no intention to give chase, and Clair sees that Sneasel has successfully snatched into its hands a reddish rectangular piece.

Silver explains that Thief is one of Sneasel's most proficient moves, and the way the Koffing handled this item makes him think it must be of much importance. The boy then remembers something, and reaches into his pocket for a tiny metallic badge, which he flicks back to Clair. He explains that he stole it from her some years ago, also with the aid of Thief, and it seems like the perfect chance to return it now. The Blackthorn Gymleader looks into her palm to see that it is the Rising Badge which she is in charge of, and doesn't know if she should feel thankful or angry about it.

Sneasel hands over the rectangular piece to Silver, and after pondering for a moment, the boy requests to know what the phone call between Lance and Clair was about. Clair states that she has no idea, and says she only managed to catch scattered words and phrases before the signal interference completely broke their conversation. Vaguely, she could hear the words 'Safari Zone', 'Plate', and 'Arceus', which didn't seem to make any sense to her. Silver puts on a baffled look, and remarks that while he knows the Safari Zone is the new facility recently opened just west of Cianwood City, he has never heard of 'Plate' and 'Arceus'. He asks Clair what they are, but Clair barks that she already said she is just as clueless. Silver takes a look at the rectangular piece at hand, and wonders if it could possibly be the 'Plate'.

Just then, Clair notices a change in the air and alerts Silver to Murkrow and Sneasel, who are starting to tremble and shake. In a blinding flash of light, Murkrow evolves into a Honchkrow, and the Dusk Stone which it is grasping gradually fades away. At the same time, Sneasel has also evolves into a Weavile, and its hold-item, a Razor Claw, slowly disappears.

As the two check out their new bodies with shock and curiosity, Silver comments that the power and experience they have stocked up from previous battles have interacted with the items they held, giving them brand new appearances. He states that something has surely been set into motion, and their evolution is probably bound to happen in this current string of events. Deciding to head to the Safari Zone next, Silver clings onto Honchkrow, and goes airborne once again.

Meanwhile, inside the Cliff Cave, troops of Team Rocket grunts assemble underneath the commanding chamber, which is on a raised platform lined with giant stalactites. Sitting on a highchair in front of a huge computer monitor, Jagura counts to a 100, and is grateful that they have reached their goal in the number of areas to conquer. He grins that when he gets serious, he can achieve anything, and it is clear that he deserves the leader position that he sought after three years ago. To gain this title, he has gathered all the scattered remnants of the organization across the nation, gotten ready the necessary weapons and tools, and left hints here and there to foreshadow their resurrection.

He giggles that he alone will be in command now, and no matter who returns, they will not be able to dethrone him, whether it is his previous comrades or the former leader, Giovanni. However, his claim is quickly challenged, and a voice comes out of nowhere to say otherwise. Without warning, an Arbok lurks upon Jagura, and lifts him away from the highchair by wrapping its tail around his throat. The voice pities Jagura's arrogance, and sighs that he should have practiced his manners more humbly as one of the former Beast Warrior Trio, secret agents serving directly under Giovanni.

Arbok then brutally hurls Jagura off the platform, and the little man crashes onto the ground among the startled grunts, panting and trembling from the impact of the fall. Four silhouettes materialize out from behind the stalactites, and the voice remarks that Team Rocket belongs to Giovanni and exists solely because of him. Only people who continue the legacy of the great man are allowed to be in command of the organization, which is why from now on, the four of them shall be in charge of Team Rocket.

With that, the four silhouettes show their faces, revealing themselves to be Archer, a turquoise-haired guy in white; Ariana, a chubby red-haired woman in white holding a fan; Proton, a green-haired guy in black; and Petrel, a purple-haired bearded guy in black; collectively known as the Four Generals…