Cilan and Pansage are in Johto together after parting ways with Ash and Iris, but find themselves lost in the woods. They make it out safely and discover a beautiful lake, where Cilan sees a Qwilfish and tries to catch it by fishing. However, the line accidentally hooks a Gyarados that Cilan decides to capture as well. He has Pansage use Bullet Seed and Rock Tomb to weaken Gyarados, then orders a Solar Beam to finish it. Pansage charges energy from the sun and leaps to attack Gyarados at close range, but is hit by Gyarados's Flamethrower and injured. Worried about Pansage, Cilan calls off the battle and decides not to catch Gyarados. Gyarados is suddenly shocked by blue electricity and fires a Hyper Beam before diving into the lake and swimming away. Cilan is surprised by the Gyarados's actions, but turns and rushes to a Pokémon Center. In a street corner along the way, Cilan comes across Brock, who lets him go by. Cilan continues running to the Pokémon Center as Brock watches.
At the Pokémon Center, Cilan tells Nurse Joy about the incident with the Gyarados and its Flamethrower. Brock walks in and offers to help with the treatment, and Nurse Joy thanks him. Pansage is sent to a treatment room as Cilan anxiously waits for him to recover. After a while, Nurse Joy comes back out and tells Cilan that Pansage is fine and just needs some rest, which Cilan is very relieved to hear. Nurse Joy asks Cilan why he tried to catch the Gyarados from the lake, and he explains that he hooked the Gyarados while fishing. Nurse Joy says that this particular Gyarados is called the master of the lake and has a very powerful Hyper Beam, which Pansage is lucky to have avoided. Cilan says he saw Gyarados glow and fire a Hyper Beam after he had given up catching it. Shocked, Joy says she has never heard of such behavior in a Gyarados. Brock exits the treatment room and says his work is done, and Cilan and Joy thank him. Nurse Joy remarks that Brock is very skilled, but he admits he is still inexperienced and has much to learn. With the situation finally calm, Brock begins to flirt with Nurse Joy, prompting Croagunk to come out of his Poké Ball, stun Brock with Poison Jab, and drag him away.
A young girl enters the Pokémon Center and calls for Nurse Joy, so the group heads to the lobby. Joy asks the girl, Ayumi, what is wrong while Cilan and Brock stare at her Pikachu. Ayumi is worried that something might be wrong with her Pikachu since she cannot use Thunderbolt well. Brock and Cilan examine Pikachu, focusing on her heart-tipped tail, and see nothing wrong. Cilan introduces himself as a Pokémon Connoisseur and gives Pikachu some Pokémon food. He deduces that Pikachu and Ayumi are really close, but this issue may be from a lack of practice. Ayumi is a bit confused at first, but Cilan explains that newly-learned moves require practice in order to work. He offers to help Ayumi with a battle, who happily accepts.
On the battlefield, Ayumi tells Pikachu to use Thunderbolt on Cilan's Stunfisk. Pikachu tries hard, but is still unable to hit Stunfisk. Cilan tells the two to relax and take deep breaths. Once again, Ayumi has Pikachu use Thunderbolt, but this time it manages to make contact with Stunfisk, who giddily enjoys absorbing electricity. Brock comments that Cilan's advice worked perfectly, and asks if he is from the Unova region. Cilan confirms this and adds that he recently came to Johto to study afresh as a Connoisseur. Brock offers to cook a meal for Cilan, which he accepts. Later, the group have a picnic with bowls of Pokémon food for Stunfisk and Pikachu. Ayumi and Cilan praise Brock's soup as soon as they taste it. Brock mentions it has been a while since he has cooked for others and that he used to cook for friends he went on a journey with. Cilan comments that he did the same and wonders how they are doing.
Back at the Pokémon Center, several people have come because their Pokémon were injured by Gyarados, adding that Officer Jenny is trying to keep the Atrocious Pokémon under control. Nurse Joy rushes the Pokémon to treatment rooms, and Brock tells Ayumi to head home so her parents will not worry. Cilan offers to walk her home and will check out the situation afterward. Outside, Gyarados makes its way down the city's river as Officer Jenny has people evacuate and find shelter. She has her Growlithe use Flamethrower on Gyarados, but it counters with Hydro Pump and then swims away with Officer Jenny in pursuit. The Qwilfish from before, revealed to actually be a robot, reappears in the water along with a mysterious man in a boat. He takes it out of the water and attempts to think of another plan to catch Gyarados.
Officer Jenny manages to trap Gyarados between some steel gates at a plaza on the opposite side of the river. Gyarados tries to destroy the gates with Flamethrower, but it is no use. Gyarados then prepares to use its Hyper Beam, but Cilan shows up just in time to tell Gyarados to stop what it is doing. Officer Jenny tells Cilan to step back, but he says Gyarados is only acting this way because he tried to catch it. Gyarados suddenly attacks with Flamethrower, but Growlithe counters with its own Flamethrower before Gyarados swims away.
Cilan, Brock, Nurse Joy, and Officer Jenny regroup at the Pokémon Center to come up with a plan to return Gyarados to the lake. Since Cilan is also a Fishing Connoisseur, he says he will handle the wrangling of Gyarados himself. Brock then takes him to the recovery room and says he will bring Pansage to him once he has recuperated.
Officer Jenny takes down the gates she used to trap Gyarados at the plaza, then hops into a boat with Cilan in tow. Once Cilan successfully lures Gyarados using his fishing rod, a net is released from the back of the boat to trap it. With the boat dragging it, Gyarados is unable to use its attacks to break the net. Officer Jenny then begins to drive from the city's river to the lake. They pass by Ayumi's house and she wishes them good luck. Afterward, Cilan once again sees the Qwilfish and realizes it is actually a robot. The robotic Qwilfich shocks Gyarados, explaining the blue light Cilan saw earlier. Officer Jenny spots the mysterious man and reveals him to be Amer, a Pokémon poacher who catches Pokémon by illegal means and sells them for profit. Amer reveals that he is after Gyarados because it can use Flamethrower, making it a rare find. Amer use a remote to have the Qwilfish robot cut the net off Officer Jenny's boat, and then he attaches the net to his boat and takes off with Officer Jenny and Cilan in close pursuit. Ayumi witnesses Amer's capture and, worried for Gyarados, runs to get help.
With all the injured Pokémon at the Pokémon Center now healed, Brock tells Pansage he will take him back to Cilan. Just then, Ayumi rushes in and tells Nurse Joy and Brock that Gyarados is in trouble. Outside of the city, Gyarados tries desperately to escape from the net and Amer fires missiles at it using his robotic Qwilfish. Gyarados finally breaks free from the net with a powerful Flamethrower, but is shocked by Amer's Qwilfish Amer and ends up sinking into the river. Amer thinks Gyarados has finally given in, but then it emerges from the water and uses Hyper Beam to destroy the robot. Gyarados begins giving off a red aura, which Officer Jenny identifies as the move Outrage. Gyarados destroys Amer's boat using Flamethrower, so Amer attempts to make a run for it, but Cilan sends out Crustle to stop Amer with a heavy body slam.
Cilan and Officer Jenny get on a bridge and try to talk to Gyarados to calm it down, but this does not work. Brock and Nurse Joy show up with Pansage, who runs to Cilan and hugs him. Cilan is relieved to see Pansage feeling all better. Brock laments that their voices may not be able to reach Gyarados anymore since its Outrage has been triggered. Cilan does not accept, and he runs to the side of the bridge once more to talk to Gyarados, but this fails again. Brock then notices that Gyarados is wounded on its tail and should calm down so it can be treated. With a new plan, Pansage uses Grass Whistle by pulling out a chunk of the sprout on his head and playing music. The move's effect puts Gyarados to sleep, so Brock wastes no time to climb onto Gyarados and spray a Super Potion on its wound. Later, Gyarados wakes up back in its lake and Cilan says it can now live in peace, so it leaves. Brock states that Cilan's courage reminds him of a friend he traveled with. Cilan says that he had a friend like that who must have rubbed off on him without him realizing.
Back at the Pokémon Center, Officer Jenny thanks Cilan for his help and says that Amer will be arrested. Never one to let such an opportunity go to waste, Brock starts flirting excitedly with Officer Jenny, but Croagunk Poison Jabs his efforts once again. Cilan jokingly comments that Brock is a "Lady Connoisseur" and sets off on the road. As he walks away, Cilan realizes that he never asked Brock his name, but he quickly shakes it off.