Murkrow debuted in Top-Down Training!, where Paul used it in a battle against Cynthia's Garchomp. It launched a Haze, which Garchomp easily dodged. It proved far too much of a lightweight to tackle Garchomp, as a collision between Sky Attack and Garchomp's Giga Impact knocked it out in one blow. Whilst it recovered with Weavile, Torterra, and Chimchar, Paul revealed that it was caught during his journey through Kanto, Johto and Hoenn.
In Glory Blaze, Murkrow used Shadow Ball and Sky Attack to try to force Chimchar's Blaze to activate. In Riding the Winds of Change, it chased away a horde of Gligar.
It evolved off-screen between Riding the Winds of Change! and Lost Leader Strategy!. It battled Maylene in a flashback, easily defeating Meditite with Sky Attack, and then clashing with her Machoke and overpowering it.
In Aiding the Enemy!, it battled Turtwig. It charged up a Sky Attack, but the charge up time allowed Turtwig to hit with Energy Ball. Turtwig managed to dodge Sky Attack and Night Slash, but Honchkrow managed to reverse its angle and struck with another Night Slash. It also hit consecutive Aerial Aces. Just then, Turtwig evolved into Grotle, but Paul and Honchkrow were undeterred and continued their onslaught of Aerial Ace, which Grotle was unable to dodge due to its drastically increased mass and reduced speed. Honchkrow powered up and struck with a Sky Attack, Grotle stumbling and allowing Honchkrow to strike. A final Dark Pulse was enough to finish off Grotle, severely damaging Grotle's self-esteem.
In Pursuing a Lofty Goal!, Paul entered it in the Squallville PokéRinger competition. It was immediately put up against the reigning champion, Provo and his Dragonite. However, Paul and Honchkrow immediately proved to be deadly opponents as Honchkrow outflew Dragonite at every turn and dodged its powerful Fire Punch and Dragon Pulse. It managed to get the ring before Dragonite, but dropped it when Dragonite's Dragon Rush landed a hit. Both Pokémon raced for the ring, Honchkrow got it first and raced for the goal. As Dragonite prepared another Dragon Rush, Paul had Honchkrow ride the wind and land a Sky Attack, which knocked out Dragonite thanks to Honchkrow's Super Luck Ability. With a knockout, Paul won the round easily. It was also shown defeating a Swellow and Steveland's Skiploom to reach the final.
In the final round, it battled Ash's Staravia, who managed to beat it to the ring. However, Honchkrow attacked with Sky Attack and crashed against Staravia's Brave Bird, which caused an explosion which damaged Staravia more than Honchkrow, but Staravia managed to hold onto the ring and recovered. Honchkrow managed to cause Staravia to drop the ring with a Dark Pulse, but Staravia recovered. Riding the wind, Honchkrow struck with Aerial Ace and took possession of the ring, but lost it again when Staravia used Quick Attack to steal it straight out of Honchkrow's beak. Honchkrow struck with a Sky Attack and then, anticipating that Ash would counter with Quick Attack, Paul ordered Honchkrow to dodge and flatten Staravia with a Night Slash.
As Honchkrow prepared a Sky Attack to finish Staravia, he evolved into Staraptor and reclaimed the ring. Honchkrow managed to knock the ring out of Staraptor's beak, and stalled Staraptor by using Night Slash. However, Honchkrow took a beating from Staraptor's newly learned Close Combat, and then, the two clashed with Sky Attack and Brave Bird once more. Staraptor managed to recover quicker this time and chased Honchkrow to the ring. Just as Honchkrow was about to close its beak on the ring, Staraptor swatted the ring onto the goal with his wing, meaning that Honchkrow came second. On the ground, Paul lay the blame for the loss on Honchkrow, saying that its response time was too slow.
It was used to battle Ash as Paul's fourth Pokemon in Pedal to the Mettle!, where it fought Grotle again. Everyone knew that Ash putting Grotle up against Honchkrow to avenge its loss was a mistake, but Ash persisted. Shielded by Electabuzz's Light Screen, it managed to block the hit from Energy Ball. Honchkrow used Haze to blind Grotle, and then hits with another Night Slash. When Grotle used Synthesis, Honchkrow used the delay to charge its Sky Attack, which crashed against Rock Climb. Honchkrow proved far more powerful and knocked Grotle out again.
In Battling a Thaw in Relations!, it was seen at Reggie's house, along with Torterra, Ursaring, and Weavile; they were all unhappy to find out Paul had lost.