Clemont introduces our heroes to the school where he studied Electric-type Pokémon. He graduated with top honors after inventing a device that stores electricity for all to use, thanks to inspiration from his friend Shinx. Team Rocket is determined to steal that electricity, but a wild Luxio who lives near the transformer is keeping everyone at bay.
When Luxio (who evolves from Shinx) gives Clemont the cold shoulder, he has a hunch about what’s going on. He explains that just before he left school, he had planned to meet up with Shinx and ask it to come with him. Clemont never made it to that meeting, and he suspects his friend never forgave him for that.
Later, during a battle with Team Rocket, Clemont throws himself in front of Luxio to protect it. Afterward, he apologizes to Luxio and promises to meet in their usual spot the next day. When the time comes, Clemont is waiting when Luxio finally arrives, and the two of them continue their journey together!
On their journey to Coumarine City, Clemont stops to show Ash, Serena, and Bonnie an old invention of his; the "Clemontic Shower". He invites Pikachu and Dedenne to try it out, adding that the device acts like an electric shower, allowing Electric-type Pokémon to absorb the electricity they need. A familiar face approaches, Miss Éclairisse, who is a teacher at the academy that Clemont studied at when he was young. Bonnie futilely tries to arrange a marriage for Clemont, leaving her brother feeling embarrassed.
Éclairisse invites Ash and his friends on a tour of the academy. Mysteriously, as they walk off, a wild Luxio watches. After giving Ash and his friends the grand tour, Clemont recounts that it was his father Meyer who enrolled him into the academy. He adds that studying at the academy really did broaden his horizons, and he met a close friend, a Shinx, during his time. Clemont recalls that Shinx was injured from a lack of electricity. After being nursed at a Pokémon Center, Nurse Joy told Clemont that lots of Electric-type Pokémon are suffering from lack of electricity. With that, Clemont got the idea for his graduation research project, the Clemontic Showers, which he invented with Shinx and the device became a success all over town. He told Shinx of his dream to make a world where all Pokémon can be happy, a dream Shinx seemed to support.
Back in the present day, Team Rocket overhears Clemont talking about his Clemontic Showers device, and decide to use the technology to attract Electric-type Pokémon, including Ash's Pikachu. They head down into the sewers to manipulate the electricity. The trio’s tinkering leads to a blackout, which attracts the attention of Clemont and his friends, who head down with an engineer to investigate. They catch Team Rocket red-handed, and also notice Luxio. Clemont recognizes the intense gaze as the Shinx he befriended in the past. Luxio tries to attack with a Swift, but Pikachu’s Thunderbolt blocks the attempt. Ash and his friends redirect Luxio to Team Rocket. Luxio then follows Team Rocket to an electrical tower.
Meanwhile, Clemont and the others reunite with Bonnie and Miss Éclairisse in the central control building to discuss a counter-strategy against Team Rocket. The head engineer calls on Officer Jenny for assistance, and she starts scouring the underground sewers for the troublesome trio. Later the others notice Clemont is oddly distracted by something, and he admits it has to do with Shinx. Serena suspects that the Luxio they saw was indeed Clemont's friend Shinx, who has since evolved. Clemont agrees, and tells the story about how he and Shinx became separated. It was the day before his graduation and he was going to deliver a cake to Shinx and ask to catch him and be his partner. But then the mayor arrived and forced Clemont into his limo to go to a party celebrating his invention. Clemont saw Shinx soon to be disappointed as he leaves, and when he returned, Shinx had left, assuming Clemont abandoned him.
Another blackout occurs, and Éclairisse calls on Clemont to assist. She says that Officer Jenny was unable to find the culprits during her search. Clemont is certain Team Rocket are behind the mass blackout and deduces that they must be at the central tower. Meanwhile, Luxio rushes over to the central transformer tower where he confronts Team Rocket messing with the electrical supply. Jessie and James call out Pumpkaboo and Inkay to retaliate. Luxio dodges a barrage of attacks, but is knocked down by a Shadow Ball. Clemont and the others arrive at the scene, to which Team Rocket performs their motto. Luxio gets back up again, launching itself at Team Rocket with a Thunder Fang. However, Inkay manages to toss Luxio to the ground. As Pumpkaboo launches a Shadow Ball, Ash has Pikachu use Electro Ball to intervene. Clemont rushes over to Luxio, though the Electric type is determined to battle on. It reprimands Team Rocket’s actions, to which Meowth translates that Luxio is trying to make a world where all Pokémon can be happy. Clemont realizes that Luxio still holds onto the very dream they both agreed to follow while studying. Team Rocket are disturbed by the ambition and Jessie calls on Pumpkaboo to attack. Clemont steps in front, taking the Shadow Ball for his friends. After Clemont defends Luxio, Luxio remembers his friendship with Clemont as a Shinx and licks him as a sign of affection. Then Luxio fights Team Rocket and sends them blasting off with a Discharge attack.
As Luxio prepares to return underground, Clemont stops him, and asks Luxio to meet him in the Town Square if he still wants to be his partner. The next day arrives. Just as everyone is about to give up hope of Luxio forgiving Clemont, the Electric type jumps out of the bushes and allows himself to be captured, while Clemont cries tears of joy. Now they leave happily, with Clemont's new partner in hand.