It is another fine day in Johto, and Gold is busy making himself a meal in a small pot heated by Typhlo's fire. He takes a sip of the soup he's boiling, and tells Typhlo to turn up the heat. However, still not being too skillful in controlling its powers, Typhlo charges up its flames and instantly burns the whole pot of soup. Gold gets upset and decides to find something else to do instead. He wonders where Politro and Silver are, and checks on the map in his Pokégear to find himself at the Ruins of Alph. Looking over the barren ground where dated rock-built structures stand, Gold suddenly spots a girl with purple hair crouching next to her Metapod and immediately walks over to flirt.

Gold introduces himself and asks the girl out for tea, but it turns out that the girl is actually a young boy, and he introduces himself as Bugsy from Azalea Town. Gold tries to sound cool after making a fool of himself, and asks what Bugsy is doing at the ruins. Bugsy explains that he is a member of the Johto Ruins Investigating Team, and that he is currently searching for his other teammates who have lost touch with them since yesterday. Gold remarks that one of his Pokémon has gone missing earlier as well, and Bugsy informs Gold that there have been reports of missing Pokémon in the nearby Johto Fishing Resort as well. Just then, Aitro seems to hear voices and puts its ear next to a huge block of stone at the base of one of the ruin buildings. Gold wonders what it has heard and quickly calls Typhlo forward.

Bugsy gets freaked out when Typhlo blasts through the stone blocks with its flames, and says they shouldn't destroy the remains of Johto's ancient culture. But Gold points out that the voices might have been Bugsy's missing teammates, and jumps into the opening Typhlo created. Bugsy is unsure about what they're doing, but decides to follow anyway calls out her Heracross. As the two walk along the corridors of the ruin chambers, Gold spots odd markings on the walls everywhere. Bugsy suddenly thinks of something and quickly flips through his research notebook. He tells Gold that the Ruins of Alph are believed to be constructed 1500 years ago, and that mysterious beings known as the symbol Pokémon were rumoured to exist back then.

Bugsy points out that no one has actually seen those Pokémon, but he assumes that the odd writings on the walls must tell something about them. He goes on to say that humans and Pokémon are said to have co-existed for a very long time, and he might be able to deduce just how long by decoding the writings on the walls. Gold remarks that Bugsy is getting too occupied with his fantasies, and reminds him that they still have to find his missing teammates. Bugsy laughs embarrassedly and resumes their search.

Suddenly, silk threads shoot out from the other end of the chamber, and instantly wrap themselves into cocoons around Gold and Bugsy. Gold wonders what is going on, and the TR Elite Trio appears with their Elekid, Girafarig and Spinarak. Ryu thanks Gold for leading them to the chamber which was supposed to be accessible only after a puzzle is solved at the entrance, and says in order for Team Rocket to make a full come back, they will need to capture the symbol Pokémon. Bugsy is surprised that the evil organization in Kanto disintegrated three years ago is being resurrected, and Gold notices that Typhlo is trapped by the silk threads as well and cannot unleash its fire attacks.

Ken orders his Elekid forward to threaten gold with its electric sparks, and Gold pretends to surrender when Aitro secretly reaches its tail into his backpack for a Pokéball. Gold's newly captured Sunkern, named Sunflo, pops out and delivers a flash. This blinds everyone in the room momentarily except Gold, who has Aitro help him put on his goggles when Sunflo unleashed its attack. Gold quickly unties himself and Bugsy, then notices that the odd markings on the wall start to wiggle and come off. He takes out his Pokédex, which recognizes them as Unowns, and gasps in shock when he realizes that the markings aren't writings about the symbol Pokémon but are the Pokémon themselves. Bugsy rationalizes that it must be the flash attack that awakened them, and ushers Gold to flee as more Unowns come off the wall and start chasing after them.

Ken, Ryu and Harry recover from their momentary blindness, and gasp in surprise to see the Unowns coming alive. Ryu grins that there isn't another way out in the chamber, and says he knows of a way to deal with the two boys first before capturing the symbol Pokémon. Meanwhile, Gold and Bugsy are having trouble finding an exit, and suddenly hear the faint whispers of people again. Bugsy recognizes the voices as those of his teammates, and says they must be in the adjacent chamber right next to them. The two follow the wall to search for an opening, but soon find their way blocked by a giant spider web. Bugsy takes out his magnifying glass, and with his profound knowledge in bug Pokémon, recognizes the web as silk threads created by Spinaraks. He warns Gold that the silk threads used to make webs are much stickier than the ones that wrapped around them earlier, and suggests finding an alternative path. However, as the two wander around the chamber, they soon discover that all the openings have been sealed by spider webs.

Gold hears both the footsteps of the TR Elite Trio and the swift movement of Unowns closing in on them from opposite directions, and quickly thinks of a strategy. Harry laughs that Gold and Bugsy should now be caught in the spider webs they set up, and hurries with the Ken and Ryu into the chamber where the boys are. To their surprise, the room is filled with smoke and they find the Unowns being trapped in the web instead. The Unowns get enraged and unleash a powerful blast of energy, instantly fainting the TR Elite Trio and their Pokémon. The Unowns then start returning to the chamber walls, and Gold and Bugsy slowly climb out from their hiding spots. It turns out that Gold has made use of Typhlo's smokescreen to blind the Unowns and lure them to the spider webs, while he and Bugsy crouch in the corner of the chamber to wait for the TR Elite Trio to approach.

Later, the missing members of the investigation team have all been found, and Bugsy thanks Gold for his help. Bugsy feels fortunate to be finally able to witness the Unowns, and remarks that according to information they have, the powerful attack the symbol Pokémon unleashed was probably hidden power. He goes on to talk endlessly about the many possible things they will be able to learn from the new findings again, and Gold sweatdrops at his enthusiasm before thinking hard for a reason to excuse himself. Gold waves goodbye to Bugsy as he continues on his journey with his Pokémon, and Bugsy wishes him good luck.

Meanwhile, the TR Elite Trio are still in the ruins chamber and trying to find a way to solve the puzzles, in hopes of awakening the Unowns again. Yet they find themselves clueless about the baffling stone blocks, and curse the ones who wrote the equally indecipherable hints next to the puzzles. Just then, their communicating device beeps and a voice comes on to mock them of their failure again. Ken demands to know who is calling, but the voice on the other side coldly remarks that it is common sense to speak to one's leader with politeness. Ken realizes with a start that it is their new team leader calling in person, and quickly apoligizes for his arrogance…

Thanks To Coronis For Writing this for us