During a thunderstorm (literally caused by angels bowling), Homer tells a scary story to his children, and a homing pigeon named Raymond Bird by his owner flies through Bart's window and breaks his wing. Unable to give him back to his owner (due to his laziness to get it back), Lisa reveals that she has ornithophobia so it is up to Bart to nurse the bird back to health with her instructions. As the bird regains his health, Bart bonds with Raymond. He finds out that the pigeon can be used to send messages between people, which leads everybody to enjoy their time with the pigeon, minus a disgusted Lisa (the only time that she even tries to get contact with the pigeon only reinforces her phobia, since Raymond regurgitates on Lisa's arm). The exhausted bird, however, gets eaten by Santa's Little Helper, and Homer and Bart's attempt to retrieve Raymond from Helper's mouth backfires when the little bird falls back into the dog's mouth and slips into his stomach twice, (the first time where Bart tries to get the bird out) where he's instantly digested.
After a symbolic funeral, Bart (who even cries) has a hard time coping with the loss and becomes so mad at Santa's Little Helper that he starts to act coldly towards him, leaving Homer and Marge worried as they are aware that Bart has trouble forgiving people even for the smallest offense (evident by the fact that he still had not forgiven Milhouse for breaking his toy car, believing it to be a Transformer). When they take him to a therapy session with Dr. Thurmond (voiced by guest star Rachel Weisz), she tries to convince Bart that Santa's Little Helper is an innocent creature who never had the intention to hurt him and that Bart should forgive him. When this fails (thanks in no small part to Helper's taste for birds) she advises the Simpsons that the only cure for Bart’s blues is to give away the family dog, leaving Lisa mad at Bart for forcing them to abandon their beloved pet. They take him to an ostrich farm up state. Bart bids a tearful goodbye to Santa's Little Helper and tells him to never kill a bird. Homer manages to get into a fight with an angry and sociopathical ostrich which then turns on Bart.
After being told that it is wrong to kill birds, Santa's Little Helper ceases to aid Bart in the fight, confused at his own loyalty (for Bart's sake or his orders) leaving Bart to strangle the ostrich to near-death in exactly the same manner Homer strangles him (leaving Homer proud of his son). Bart then realizes that Santa's Little Helper could not help what he did and apologizes for holding such a grudge against him. The family goes back home with the dog and the ostrich Bart strangled tied to the car, but the ostrich regains consciousness and punches through the roof with its claw, proceeding to strangle Homer.