Rinse the soaked kidney beans and place them in a large pot with 3 cups of water. Bring to a boil, then reduce heat and simmer until beans are tender, about 1 hour.
Add the coconut milk, whole Scotch bonnet pepper, chopped scallions, thyme sprigs, minced garlic, salt, and black pepper to the pot. Stir to combine.
Bring the mixture back to a boil, then stir in the rinsed rice. Reduce heat to low, cover, and simmer until the rice is cooked and all liquid is absorbed, about 20-30 minutes.
Turn off the heat and let the pot sit covered for an additional 10 minutes to steam the rice.
Remove the Scotch bonnet pepper and thyme sprigs. Fluff the rice with a fork before serving.