While heading toward Sunyshore City and Ash's next Gym Battle, our heroes get lost in a dark forest. They come across a mischievous Murkrow that creates what turn out to be fearful illusions. That Murkrow happens to be in the care of a Trainer named Mitchell, who has a sister named Rhyanna. Mitchell and Rhyanna haven't been speaking to each other since Mitchell took off into the mountains to train with his Murkrow—with the goal of finally beating his sis in battle. Now Rhyanna wants to find a Dusk Stone so she can evolve her Misdreavus into a Mismagius. She hopes the evolved Pokémon will help her brother become happy again. However, the angry Mitchell thinks Rhyanna's purpose is to keep winning battles against him!
That brings us to Team Rocket. Of course, their eyes are on getting themselves a Mismagius and a Dusk Stone, too—and what better way than to steal Rhyanna's Pokémon? With Brock's help, Rhyanna has found a Dusk Stone, which goes to the top of Team Rocket's must-steal list, along with Rhyanna's Misdreavus. But, even with Team Rocket's latest invention, the "Porta-Pidgey Mark Two" robot, the would-be thieves aren't able to hold onto Rhyanna's Misdreavus or the Dusk Stone.
Finally, Rhyanna and Mitchell discuss their issues and make up, happily deciding that the winner of the best of 10 battles between them gets to keep the prized Dusk Stone. And, happy in the knowledge that they helped to reunite the quarreling siblings, our heroes resume their journey toward Sunyshore City.
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While on the way to Sunyshore City, Ash and his friends find themselves lost in a deep forest. They suddenly see a Murkrow up in a tree then flies above their heads. Brock and Dawn worry that something bad is about to happen, as it is told in an old saying about Murkrow. Suddenly, they feel the ground shaking and are then attacked by Giratina. They escape but are caught up in a flood of rushing water. A woman rescues them and wakes them up, telling them that they were caught up in an illusion caused by a Murkrow's Confuse Ray. Brock flirts at the woman, only to be stopped by Croagunk. Ash and his friends introduced themselves to the woman's name, Rhyanna, who lives in a nearby village. She tells them that Murkrow was her brother's Pokémon and the reason why they are seeing illusions.
They start to talk about Rhyanna's brother, she told them that her brother's name was Mitchell and they used to battle together, Mitchell wants to become stronger so he trained his Murkrow in a mountain, that's when he began play pranks on the travelers. Ash and Dawn ask why she didn't put a stop to this, or talk to her brother, Rhyanna told them that she was being avoided by her younger brother that's why she's looking so hard for a Dusk Stone to evolve her Misdreavus into a Mismagius, believing from her grandpa that it can chant spells that can bring people happiness, she was planning to use it on Mitchell so that she and her brother can make up. Brock decides to help Rhyanna and promised to do everything he can to make her happy.
At a distance, Team Rocket was eavesdropping on their conversation. James took out their new gadget, a Dusk Stone detection device, and they begin to search for a Dusk Stone, hoping to find their own happiness. Rhyanna takes our heroes to a shrine, according to her grandpa, people used to mine Dusk Stones somewhere nearby the shrine, she once tried to look for a Dusk Stone before but with no success. Ash and friends decide to help Rhyanna in her search this time, the four split up into two teams with Ash and Dawn, Rhyanna and Brock, Brock suggests that maybe her Misdreavus can find it, since they were the only ones that evolve via Dusk Stone so she took out her Misdreavus. Misdreavus searches and seems to sense something. As Ash and Dawn continue their search, the same Murkrow suddenly appears and starts pecking Piplup's head, Ash commands Pikachu to use Thunderbolt on it so that they can capture it, Murkrow couldn't dodge the hit and Mitchell came running back to it, Mitchell told them that his sister doesn't care for him but Dawn instantly disagrees to what Mitchell says, and explains that his sister was even trying to find a Dusk Stone just to make him happy, which makes him reconsider.
As Brock and Rhyanna follow Misdreavus, Team Rocket's detection device lead them to falling off of a cliff, they find a mysterious cave and believe there maybe Dusk Stone's inside of it, they have a quick fantasy about giving a Mismagius to their boss and in turn realize in order to have a Mismagius, they should also have to catch a Misdreavus. Suddenly, they caught sight of Rhyanna's Misdreavus just before Rhyanna and Brock themselves falls off the same cliff. Ash and Dawn are chasing Mitchell. When Ash finally catches up to him, Mitchell says he wants to get the dusk stone before his sister does. He explains to Ash and Dawn that he wants to become stronger so that he could beat his sister, so he trained up in a mountain with Murkrow, though when training, Mitchell pushed Murkrow too hard by continuously pelting it with stones and denying it the chance to recover when it got hit, which caused Murkrow to run away from Mitchell and stop listening to him. Ash and Dawn realize Mitchell has nothing to do with any of Murkrow's pranks. Mitchell continues blaming his sister for everything, but Dawn tells him to look at how his Pokémon feels. Ash, feeling the same way, tells Mitchell that the only way to become stronger is to work with Murkrow as a team and start listening Murkrow's feelings instead of just his own. Mitchell, now realizing that he'd hurt Murkrow out of his own frustrations of not being able to beat Rhyanna, feels sorry for how he treated his Pokémon, and tearfully apologizes to it, which wakes it up.
Rhyanna and Brock finally wake up and find themselves in a place where her Grandfather used to mine for dusk stones, Misdreavus detects something below a large rock, and when Brock removes the rock, they find themselves a dusk stone. Rhyanna cheerfully embraces and thanks Brock for his hard work, while Brock is thrilled and blood-red, Team Rocket suddenly appears and catches Misdreavus, reciting their motto after wards, Brock quickly sends out his Sudowoodo and commands it to save Rhyanna's Misdreavus, Meowth pulls out a remote that controls a Pidgey robot, Ash, Dawn and Mitchell saw the robot fly above their heads and rushed to where Team Rocket were, Meowth throws Misdreavus into a cage located in the Pidgey robot's chest, Team Rocket attempt to escape in their giant robot, Brock commands Sudowoodo to use Double-Edge, Meowth sends out a fan that blows away Sudowoodo, Brock commanded it again to use Double-Edge at the robot, the Pidgey robot sends out a broom, twirling it and using Sand-Attack to stop Sudowoodo, the robot then fired its right wing to Sudowoodo, which knocks it unconscious, Brock returns Sudowoodo.
A robotic hand tries to snatch away Rhyanna's Dusk Stone, Rhyanna doesn't want to let go, the robot then flies up into the air with her still attached. Ash and Dawn, with Mitchell see this, Mitchell realizes that he was wrong about his sister after seeing her determination, Pikachu was ready to use Thunderbolt but stopped by Ash, Ash took out his Staraptor and commanded it to help Rhyanna, Mitchell sends out his Murkrow to help her too, Murkrow followed him after Mitchell begs it to return its trust to him again. Staraptor got Rhyanna's shoulders with Murkrow using Peck on the robotic hand that got Rhyanna's dusk stone. The robotic hand broke off and Rhyanna got her Dusk Stone back, Staraptor safely landed with Rhyanna but Team Rocket still has Misdreavus, Mitchell commanded Murkrow to get it back and successfully returns Misdreavus with no trouble, Ash commands Pikachu to use Thunderbolt which blasted Team Rocket again.
Mitchell and Rhyanna were once again reunited and were happy to see each other, Rhyanna told him that she doesn't need to evolve her Misdreavus because Mitchell doesn't need to have a happiness spell anymore. Mitchell then challenges Rhyanna and says that whoever wins the most battles out of ten gets the stone, Rhyanna happily accepts the challenge. A little help from Ash and friends settles the disagreement once and for all, and now that Ash has drawn a training inspiration from new friends, the journey continues...