Pookie's only appearance in the comic series was the story "Bowser Knows Best". Pookie can be seen cowering in his cage in the first page of the comic, while the Koopalings are deciding what to get their father, Bowser, for Father's Day. Roy suggests that simply beating Pookie would be a suitable present for Bowser.
Roy later accidentally drops and breaks Pookie's cage when Wendy forcibly drags him away to help her and the others capture Princess Toadstool. Free of his cage, Pookie hops away, and can be glimpsed a few times wandering through Bowser's Castle.
Pookie later appears on the last page of the story, while Bowser is distracted reading a calendar which Lemmy had written (rather poorly) "Be Kind to Turtle Kid Day" (a fake holiday made-up by Princess Toadstool) on. Pookie manages to escape his owners by jumping out a window, just as Roy realizes he is missing.