Stormy Weather is episode 3 in season 2.
Courage is outside licking a bone when he sees a crying woman with a rain cloud hovering over her. The woman quickly spots Courage and excitedly runs towards him, scaring the dog. Before Courage can run into the house, the woman quickly grabs him at the door and starts hugging him lovingly before she attempts to play fetch with him using a ball. Muriel comes out and assumes Courage has made a friend with this woman. Muriel then invites her inside for a cup of tea despite Courage's pleas for her not to. At the table, the woman (who reveals herself to be a goddess) talks about how her life isn't always heavenly. She goes on to explain that she lost her dog Duncan and how Courage reminds her of Duncan. The Storm Goddess shows a picture of the dog, revealing that he looks like Courage, but smaller and skinnier. As the storm hovering over the goddess gets a little stronger, Muriel goes over to shut the window due to thinking its wind from outside. As she turns around, she sees the goddess hugging Courage. The goddess asks would Muriel mind if she took Courage outside for some air, and she walks out without even waiting for Muriel's reply (which was that she did in fact mind). Later that day at dinner, Muriel is no longer as welcoming to the goddess (who is still being overly affectionate to Courage). When the Goddess announces her plans to take Courage with her, Muriel begins arguing with the goddess, both claiming ownership to Courage. The goddess' anger eventually destroys the house and blows Eustace away. Courage fearing for Muriel's life, decides to let the storm blow him away so he can go find Duncan.
Courage goes to various places around the world during his search, though none of the people he meets have seen Duncan. Returning to Nowhere, Courage goes to a restaurant where Charlie the Mouse recognizes Duncan from the picture. Charlie tells Courage that he saw Duncan go down in the sewer. Courage wanders the sewer and gets on a boat which takes him to the gargantuan bone known as the God Bone. A mysterious voice warns against licking the bone for those who lick the bone become addicted to it and are unable to stop licking it. Courage hears the sound of licking and begins running around the bone, finding the skeletal remains of dogs. Eventually, Courage finds Duncan licking the bone. Courage tries to pull Duncan, but not only is Duncan strongly attached to the bone, Courage too starts to suffer from temptation of the bone and starts licking it. As Courage starts to lose himself in the bone, Courage reminds himself of Muriel's peril and potential death and begins trying various methods of getting his tongue off the God Bone. After failing with a metal claw and jack, Courage uses a feather to tickle his tongue off the bone and then wraps it in a knot before putting it back in his mouth. Courage carries Duncan and the bone out when the Dog Skeletons come to life and they go after Courage. Upon catching up to a tired Courage, they begin beating him on the head with their bones. As they attempt to drag Courage back to the God Bone's original spot, Courage frees himself, grabs the huge bone, and smashes the Dog Skeletons to pieces. Using the bone again, Courage drills a hole through the ceiling and digs his way back to the remains of the Bagge house where Muriel and the Storm Goddess are still arguing over Courage's ownership.
The Storm Goddess is happy that Duncan is back, but upon seeing his lack of reaction to her and his continued focus on licking the God Bone, she assumes that Duncan loves the bone more than her. Crushed, she once again puts her focus on Courage, grabbing him and cuddling again to his displeasure. Getting an idea, Courage begins returning the goddess' affection, hugging her back and licking her face. This display starts to make Duncan angry until he finally breaks free of the God Bone's addictive hold and forces Courage away to be with the goddess. Both happy to be together again, she then walks away from the Bagge residence with Duncan in her arms . Sitting in her chair inside the house remains with Courage in her lap, Muriel is glad everyone got what they wanted. Courage agrees and reveals he still has the God bone and happily licks it.