In the film prequel, the Scarecrow's origins are explained; he was one of the scarecrows being fabricated by the townspeople of Oz as a false scare tactic during the retaliatory attack on the Emerald City.
When Dorothy left Oz, the Scarecrow became the king of Emerald City, but the Nome King took over the land with the aid of Mombi by imprisoning the real ruler Princess Ozma and using Dorothy's ruby slippers to turn everyone into stone. The Scarecrow avoided this, but was imprisoned by the Nome King. After Dorothy encountered him in the Nome King's mountain, he disappeared and was turned into an ornament by the Nome King. He is freed from this form by Dorothy while trying to free the Nome King's prisoners and they reunite. He helps her find Tik-Tok, Jack Pumpkinhead, and the Gump. Unfortunately, the Nome King arrives, and is angered by being nearly beaten and tries to eat the group, starting with Jack. However, Billina appears in Jack's head and lays an egg that falls right into the Nome King's mouth, killing him, as eggs are poison to Nomes. Quickly, Dorothy uses the ruby slippers to return her, Jack, Scarecrow, Billina, Tik-Tok, and the Gump back to the Emerald City and free the Ozians from the stone curse. Scarecrow celebrates along with his revived friends to Dorothy's victory, and witnesses the return of Princess Ozma. He says goodbye to Dorothy as she departs from Oz once again, but knows that she can return anytime if she wants.
The Scarecrow appeared in the episode Our Decay. He is captured by a flying monkey, and brought to Zelena, the Wicked Witch of the West. Needing his brain for a time-travel spell she plans to enact, Zelena is about to remove it when suddenly Dorothy arrives, now an adult. He runs behind her from protection, and the pair flee together. The pair camp together outside a building, and when the Scarecrow comes out from there, he is shocked to find Zelena. She freezes Dorothy so she is no longer able to protect him, and rips out his brain.