Combine the fish chunks with lemon juice, turmeric powder, red chili powder, and half a teaspoon of salt in a bowl. Toss gently to coat and set aside for 20 minutes.

Rinse the basmati rice until the water runs clear and soak in water for 30 minutes, then drain. Bring a large pot of water to a boil with the cinnamon stick, green cardamom, cloves, and 1 tablespoon of salt. Add the soaked rice and cook until it is about 70 percent cooked with a firm bite in the center, then drain well.

Heat 1 tablespoon of ghee in a heavy-bottomed pot over medium heat. Add the sliced onions and cook, stirring frequently, until golden brown and crisp at the edges. Remove half of the onions for garnishing.

In the same pot with the remaining onions, add the ginger paste and garlic paste and cook for 1 minute until fragrant. Add the chopped tomatoes, garam masala, and cook until the tomatoes soften and oil separates slightly. Stir in the whisked yogurt.

Gently nestle the marinated fish pieces into the masala. Cook over low heat for 5 minutes without stirring aggressively, until the fish is just beginning to turn opaque.

Spread the partially cooked drained rice evenly over the fish masala. Top with the reserved fried onions, chopped cilantro, mint leaves, and remaining 2 tablespoons of ghee. Cover the pot with a tight-fitting lid to seal in the steam. Cook on very low heat for 20 minutes before serving.