Honchkrow, as a Murkrow, first debuted in Pester Control!, where he stole food from the group, using Haze to get away. He later encountered the group again while they were having dinner and stole their food once more. The group then gave chase and managed to corner Murkrow in a clearing. There, they learnt that Murkrow was giving the food to an injured Starly in order to build its strength.
After Lewis healed Starly with a Potion, Starly thanked both Lewis and Murkrow and flew away. Lewis praises Murkrow, who reluctantly thanks Lewis for the help. Lewis then challenges Murkrow to a battle, who accepts. Murkrow made good use of Haze to hide itself from Aipom, who took several powerful hits from Wing Attack. Eventually, Aipom was able to strike Murkrow with Focus Punch, sending it flying into a tree. Lewis used the opportunity to throw a Poké Ball and catch Murkrow.
Murkrow was used to help train a wild Piplup in Shock to the System!, providing some target practise while she attempted to learn Ice Beam.
In Mine Away Home!, Murkrow was sent out as Lewis' second Pokémon in his Gym battle against Roark. He battled against Roark's Onix and was able to land a few early hits with Wing Attack using Haze as a cover. However, Onix was quickly able to blow away the smoke and land a hit on Murkrow with Iron Tail. Using this to their advantage, Lewis commanded Murkrow to use Assurance, dealing more damage to Onix due to Murkrow having been hit immediately prior. After Onix used Harden to boost its Defence, Murkrow had a harder time dealing damage and was eventually defeated by Stone Edge.
Murkrow was Lewis' first Pokémon in his Gym battle against Gardenia in As Green as Grass-Types! He battled against Gardenia's Turtwig, who proved to be a powerful opponent. Murkrow initially had a difficult time against Turtwig, as the Grass-type used Double Team to avoid Murkrow's attacks and then strike back with powerful moves like Double-Edge and Leaf Storm. Eventually, Murkrow was able to land a hit on Turtwig with Assurance and finally knock it out with a barrage of Wing Attacks. When Gardenia sent out Cherrim, Murkrow was recalled.
He was sent out later on in the battle to face Gardenia's final Pokémon; Roserade. He was able to prevent Roserade from using a sunlight-boosted Solar Beam by using Haze to block the sun. Murkrow was then able to land a few hits with Wing Attack before being defeated by Poison Jab.
While training with Lewis in Gale-Force Bravery!, Murkrow managed to learn Aerial Ace. When the group later encountered a family who were taking shelter from a storm. The father of the group gave Lewis a Dusk Stone, in case he wanted to evolve his Murkrow in the future. Later, when the storm hit, a group of wild Pokémon were being buffeted by the gale at the edge of a cliff. Murkrow expressed a desire to save them, but the strong winds made it difficult for it to fly and it was sent crashing to the ground. When the wild Pokémon fell off the cliff they were on, Lewis quickly gave Murkrow the Dusk Stone so that it could evolve into Honchkrow. With his larger size and advanced flying skills, Honchkrow was able to use Aerial Ace to boost his speed and catch the Pokémon before they hit the ground. The next day, Honchkrow was used to battle the father of the family and revealed that it had learnt Dark Pulse upon evolving, using it to defeat the father's Dusclops.
Honchkrow is a relatively serious Pokémon, showing little emotion in the presence of others. He is shown to have a softer side, as shown by his desire to help an injured Starly, despite not knowing it. This softer side was also shown in Gale-Force Bravery! and it was his desire to help others that drove Murkrow into evolving. Honchkrow is also shown to be quite prideful, as seen in his reluctance when thanking Lewis for helping him. Despite this reserved nature, Honchkrow has no problem obeying Lewis' commands in battle.