Bring water to a boil in a large bowl. Add fish; simmer until soft, about 30 minutes. Strain fish, reserving broth. Let fish cool. Remove bones, trying to keep large pieces of fish intact.
Bring broth to a boil. Add green bananas, pumpkin, potatoes, corn, carrots, okra, scallions, chile pepper, garlic, salt, pepper, and thyme. Bring back to a boil. Reduce heat to low; simmer until potatoes are almost tender, about 10 minutes. Stir in fish. Simmer until flavors combine, about 5 minutes more.
Remove soup from heat and let stand before serving, about 30 minutes. Discard chile pepper.