After hearing word of the Whirl Islands, Hakel and Crystal rush off to the Islands on the back on Hakel's Pidgeot.
Meanwhile, on the Whirl Islands, Gold and Silver awaken from their slumber. Feeling a bit disoriented, they try to recall what had saved them from drowning at the Lake of Rage, however, all they can remember is some shrouded creature that healed them with its intense flames. They both remark remembering something like that and notice that they aren't ready to move around a lot because their injuries weren't completely healed. However, their time to rest was soon interrupted by a herd of Sandslash that were enraged about something, which stayed unknown to Gold and Silver.
Gold and Silver managed to escape from the cave and outside, they saw that something in the distance was coming closer to them. They soon saw that it was Hakel and the newest Johto Pokédex Holder, Crystal, whom they had not met yet.
Finally, arriving at the Whirl Islands, Hakel explained to Crystal that the reason he knew Gold and Silver were there at the Whirl Islands with just one clue was because of something eating him up inside. He didn't really understand it himself but he knew they had to be there at the Whirl Islands. Crystal didn't believe at all until she saw two Trainers that turned out to be Gold and Silver standing on top of a rock, waving to them. Crystal alerted Hakel to them and they started to fly toward them.
Right as they were about to fly over to them, a giant shadow of something passed by them and knocked Hakel and Crystal toward the water. Hakel called out his Furret at the last moment, telling it ride onto the water and Crystal called out her Natee, who kept afloat in the air above Hakel and his Furret. With Silver's help, both Crystal and Hakel were able to make onto the rock that they were standing on, happy to be back with one another once again.
Their happiness was cut short when Crystal and Hakel looked up and saw that the Legendary bird, Lugia was floating behind them, glaring with eyes full of hatred and anger. Crystal and Hakel pointed the beast out quickly, however, it wasn't enough time to dodge its next attack. Lugia sent a blast of Psychic energy sending the four of them flying through the air, letting the four of them fall into the sea. Hakel, at the last minute, called out his Pidgeot, catching the four of them easily.
Lugia then shot a blast of energy so powerful, it literally brought the sea apart when it was fired. It smashed against Hakel's Pidgeot, almost making them fall into the water again. Then, for no reason, Silver called out his Murkrow, grabbed onto its legs and flew away towards the beast.
After Silver began battling Lugia, or at least, try to see what was wrong with it, Crystal and Gold's Pokédex began to beeping. Hakel explained that it was the Pokédex Resonance System, and it only starts beeping when all the Pokédex Holders of that region are in place. Before Gold could ask another question, Lugia blasted Hakel's Pidgeot again, knocking them all off his Pidgeot into the water. Right before they splashed into the water, Hakel called back his Pidgeot.
Despite being knocked into the water, Hakel and Gold were the only ones that seemed alright. Crystal had been knocked unconscious and was being sucked into a whirlpool. Seeing Crystal in the water unconsciously, Silver called back his Murkrow and sent out his Croconaw and the two of them rode through the water to help Hakel and now, Gold save their newly acquired friend from dying. The three of them combined, they used their strength to save Crystal and set her body on a large rock to keep her safe.
Crystal woke up shortly after, and, after hearing Silver's Pokédex begin to beep, realized that they were three Pokédex Holders of Johto. Realizing that they finally met, the three Pokémon from Professor Elm's lab also met, and it would have been a joyous occasion if not for the situation. After a few more scrimmages and arguments between Gold and Silver, the three realized, with a little help from Hakel, that they had to work together to beat Lugia.
Silver started to leave but Gold made it apparent that he should stay their Pokémon, the starters, stood on the edge of the rock, ready to go into battle against the powerful Lugia, no matter what the cost would be. Against his chagrin, Silver reluctantly agreed to work alongside of Gold and Crystal, for the time being.
Exbo (Gold's Quilava), Croconaw (Silver's Croconaw), and Megaree (Crystal's Bayleef) began their attack against Lugia, however, there weren't strong enough to completely repel an attack from Lugia head on. Hakel, who had promised to stay out of the fight, used his Furret to pedal away from the blast when it became too strong for the three starter Pokémon to handle, causing another verbal disagreement to occur between Gold and Silver. Crystal managed to make them both calm down with the help of Hakel, despite their continued annoyance.
As Lugia charged up its attack again, Hakel told the three that Lugia's move was called Aeroblast, involving the power of using "air" to strike them down. He then called out his Espeon who put up a large Reflect just as Lugia fired its Aeroblast, shaking them a little.
After that was over and they had stopped moving, Silver devised a plan of bringing Lugia into the water so it couldn't form blasts of air in its mouth. They would then attack from a short distance away, which already ruled Gold out of the equation. Silver sent out his Murkrow and Crystal sent out her Natu, nicknamed Natee, and started to send them to attack. However, before they could even get close, Lugia sent a blast of air so powerful that it not only knocked Mukrow and Natee unconscious but, also threw Gold overboard, directly in the deep blue, sea around them.
Hakel had managed to bring a rope with him and, with Silver and Crystal's help, the three of them managed to toss it into the water down to him. He caught the rope in his hands but as he started to tug on the rope, a bunch of Remoraid began to bothering him about him something. When Gold turned his head, he noticed that a Mantine was frantically panicking about something. Gold let go of the rope and saw that it was one of Lugia's Aeroblasts and it was heading straight for that poor Mantine, who, for whatever reason, couldn't get away. Gold managed to save the Mantine by getting in the way of the Aeroblast, however, he started to fall unconscious because he was losing air and was far too deep to really keep conscious anymore.
Hakel, Silver, and Crystal all felt the rope get tight so the three of them yanked the rope up to the surface, however, they realized, when it came up to the surface, Gold wasn't on the other end. Just as they set down the rope and thought about going after him, they noticed a giant bubble surfacing on the bottom surface of the water. Then, the bubble exploded, and Gold burst out of the water, flying on a Mantine.
Normally, Mantine can not fly, although, Gold had tied several Remoraid to Mantine's wings, telling them to use Hydro Pump to propel themselves forward through the air to give Gold the ability to fly airily and also swim through the sea. Silver remarked that it was "a Pokémon for air and sea". Gold and his newly caught Pokémon head directly for Lugia, ready to take it down once and for all.