As seen in A Trip Down Memory Train!, Bunnelby originally lived with a group of friends inside a train car inside the abandoned Lumiose Subway. In order to help feed his friends, Bunnelby went to the surface to find food, stealing the apple Bonnie had retrieved from her house. Clemont and Bonnie gave chase, eventually falling down to the abandoned subway tunnels. Bunnelby returned to his friends, splitting the apple into even shares for his friends. After their meal, however, they were attacked by a wild Diggersby, who was trying to take the abandoned subway car as its own. While Bunnelby tried to battle Diggersby, he was clearly outmatched. Clemont grabbed Bunnelby with his Clemontic Gear's Aipom Arm, and ran away from the Digging Pokémon with Bonnie and Bunnelby's friends.
After running away, Clemont and Bonnie treated Bunnelby's wounds with a Super Potion and some bandages. Regaining some of his strength, Bunnelby immediately wanted to fight Diggersby again, but Clemont stopped him, saying the bully was too powerful to battle with a direct approach. Instead, Clemont and Bonnie demonstrated ways for Bunnelby to use his evasive skills, Double Team and Dig to dodge its powerful attack, and use his strong ears to defend himself. Challenging Diggersby to another battle, Bunnelby put these strategies to good use, defeating Diggersby, causing it to leave frustrated, refusing Bunnelby's offer to reconcile.
Bunnelby's victory was short-lived, however, as tremors began to shake the abandoned station. Clemont realized that the subway station's demolition was beginning, and that the group had to escape immediately. Discovering that Bunnelby and his friends did not want to leave their subway car home, Clemont brought out his Clemontic Gear's Running Generator, restoring power to the car, allowing them to ride the car to safety outdoors at the end of the track. Before they could get the train running, however, the track was blocked by a large boulder. Diggersby returned, using its powerful ears to move the boulder, and bashfully accepted Bunnelby's offer to help with the escape. As the train moved, Bunnelby moved to the front of the car, using his Mud Shot to help flip the train switches to direct the train to its destination.
Having arrived at a distant abandoned train station on the outskirts of the city, Clemont and Bonnie said goodbye to Bunnelby, his friends, and Diggersby, and left them to their new home. Noticing Bunnelby's sadness, his friends, including Diggersby, insisted him to join Clemont. Wiping away his tears, Bunnelby said goodbye, and ran to Clemont's side. After capturing him, Clemont called him back out, saying he was very touched Bunnelby had chosen to stay with him, and began crying tears of joy. Together, Clemont, Bunnelby, and Bonnie returned to Lumiose City.
Bunnelby was first mentioned by Clemont in Kalos, Where Dreams and Adventures Begin!, where he was said to be his most recent capture after Clemont and Bonnie were kicked out of the Lumiose Gym after it was taken over by Clemont's robotic stand-in Clembot. He was then used by Clemont to battle Ash's Pikachu. The battle started off with Pikachu using Thunderbolt, which was blocked by Bunnelby who used his ears to create a mud shield. Bunnelby then used Dig and managed to hit Pikachu, despite the latter trying to confuse Bunnelby with his speedy movements. Pikachu then scored a direct hit with Quick Attack. Bunnelby, however, quickly recovered and retaliated with Double Slap, hitting Pikachu several times before knocking him back. Pikachu then used Iron Tail which Bunnelby easily caught with its ears. Now, however, he was unable to use his ears, giving Pikachu the opportunity to hit the Digging Pokémon with Electro Ball. The battle was then interrupted by Team Rocket, who once again attempted to steal Pikachu for their plans. Bunnelby teamed up with Pikachu to try and stop the villains, but Jessie's Wobbuffet deflected Pikachu's attack and almost injured him. After Pikachu was saved by a Froakie, Bunnelby sent the trio into the air with Dig, allowing Pikachu and Froakie to blast them off.
Bunnelby was used in Clemont's Got a Secret! to battle Clemont's Heliolisk, which was being used by Clembot. Just as Clemont predicted, Heliolisk started off with a Thunderbolt and, like in his battle with Ash, he had Bunnelby create a mud shield with his ears to block the attack. Bunnelby was then able to block a Dragon Tail and after that hit Heliolisk with Double Slap. He then went for Dig, but much to Clemont's surprise, Heliolisk countered with Bulldoze. This forced Bunnelby out of the ground and was then hit by a Dragon Tail. Bunnelby then tried to confuse Heliolisk with Double Team and as he was about to launch a Mud Shot, Heliolisk countered with Parabolic Charge, dealing much damage to Bunnelby as well as healing some of its health. Clemont then had Bunnelby use Dig. As Heliolisk went for another Bulldoze, Bunnelby jumped out of the hole using Double Team, circling around Heliolisk. It was again able to wipe out Bunnelby's copies, but the real Bunnelby was still underground. This gave him the opportunity to strike Heliolisk from beneath using Dig and knocked the Generator Pokémon out with Mud Shot.
In Forging Forest Friendships!, Bunnelby was used in a Double Battle with Chespin against Ash's Froakie and Hawlucha. Bunnelby managed to hit Hawlucha several times with Double Slap, before getting knocked back by his Karate Chop. He then hit Hawlucha again with Double Slap and was about to finish it off with Mud Shot, only to get hit by Froakie's Water Pulse. Froakie then used its speed to trick Chespin's Pin Missile into hitting Bunnelby, knocking him out. Later, he wanted to eat some of Serena's Poké Puffs, only for Chespin to have already eaten them.
In A Fork in the Road! A Parting of the Ways!, Bunnelby was shown helping Clemont train for his upcoming Gym battle with Ash, defeating his Magneton in battle and learning a new unseen move.
In The Moment of Lumiose Truth!, Bunnelby was used in Clemont's Gym battle against Ash, despite the Digging Pokémon not being an Electric-type. He was Clemont's first Pokémon and went up against Pikachu. Pikachu used Thunderbolt, which was blocked by Bunnelby using his ears to create a mud shield. Bunnelby then used Dig, which was too fast for Pikachu to evade. Pikachu followed up with Quick Attack, which Bunnelby quickly recovered from. He then used Double Slap, hitting Pikachu several times before knocking him back. Pikachu then used Iron Tail which Bunnelby easily caught with its ears. This reminded Bonnie of their first battle. Instead of letting Pikachu counter with Electro Ball, Bunnelby used his new move, Wild Charge, dealing major damage to Pikachu. He then hit Pikachu with another Dig. Pikachu responded with Quick Attack, but Bunnelby used Dig again. However, Ash had Pikachu use Iron Tail on the ground, forcing Bunnelby to emerge and dealing major damage. Pikachu then used another Iron Tail, defeating Bunnelby.
In Adventures in Running Errands!, the group arrived at a Pokémon Center to shelter from the rain. A leak in the roof, however, caused the center's machinery to short-circuit. While Clemont was fixing the machine, he had Bunnelby accompany Chespin on an errand to buy a machine part. Chespin was given a purse with a letter on which the part's name was written. While heading towards the shop, a wild Fearow snatched the purse from the duo. The two eventually managed to get the purse back and escape from the Fearow. While continuing their errand, Bunnelby and Chespin got attacked by Team Rocket. They managed to hold their own against Inkay and Gourgeist. When Gourgeist attacked with Shadow Ball, Fletchinder arrived and blocked the attack, followed by Ash and his Noibat. Despite being told to stand back, Bunnelby and Chespin continued to fight Team Rocket themselves and managed to blast them off. Bunnelby and Chespin then finished their errand, giving Clemont the last part to fix the Pokémon Center's main system.
During the events of A Cellular Connection!, Bunnelby got hurt saving Bonnie from a nasty fall during the search for Squishy, and was admitted to a Pokémon Center. This left Bonnie feeling very guilty about it, and she promptly went to look for the herbs necessary to cure him. By the end of the episode Bunnelby had recovered.
In A Keeper for Keeps?, a Buneary developed a crush on Bunnelby when she returned a ball that had flown into the forest. The Buneary turned out to belong to a Trainer named Lilia, who stayed with the group for a while. During Lilia's time with the group, Bunnelby was continously seen with Buneary, holding hands as they walked, and sitting and cuddling together, much to the Digging Pokémon's discomfort. Despite these feelings, Bunnelby showed to be very protective of Buneary when Team Rocket attacked and kidnapped them. Bunnelby and Buneary were eventually found, thanks to one of Clemont's inventions, and were saved. Afterwards, when Lilia left the group, Bunnelby comforted a sad Buneary and said goodbye.
Clemont sent out Bunnelby and Chespin to combat Team Flare in Coming Apart at the Dreams!. They joined the battle against Bryony's Liepard and Aliana's Druddigon. The two of them, alongside Luxray and Heliolisk, defeated the Team Flare Scientists' Pokémon, allowing Clembot to subdue them and for the team to infiltrate the Lumiose Gym. In the following episode, Bunnelby battled with Xerosic's Crobat and Malamar, which resulted in victory and allowed Clembot to evict Xerosic from the Gym. Bunnelby was used again in Forming a More Perfect Union!, where he joined the fight against the Giant Rock. In the next episode, Bunnelby and the rest of Clemont's Pokémon received medals from Professor Sycamore for their heroic efforts against Team Flare.
In Till We Compete Again!, Bunnelby said goodbye to Ash, Serena, and their Pokémon, since they would soon separate from Clemont and Bonnie. Bunnelby was later used in one final battle between Ash and Clemont, in which he faced Ash's Pikachu, just like in their first batttle. During the battle, both Pokémon's moves proved to be equal in power, but the end result of the battle was left unknown.