Preheat the oven to 375 degrees . In a large pot, cook the bacon over medium heat until crisp; using a slotted spoon, transfer to a bowl. Add the scallions to the pot and cook until softened. Whisk in the flour and cook, whisking, for 2 minutes. Whisk in the clam juice and 2 cups water; bring to a boil. Add the potatoes and cook until tender, about 15 minutes. Stir in the heavy cream. Season with salt.
In an 8-inch square baking dish, arrange the shrimp and ladle the chowder on top, reserving 1/2 cup. Top with the tilapia; season with salt and pepper and pour the reserved chowder on top. Toss together the crackers and bacon; sprinkle on top. Bake until the fish is cooked through, about 15 minutes.