Cook the squid ink pasta according to the package instructions until al dente. Drain and set aside.
Melt the butter in a saucepan over medium heat. Stir in the flour and cook for 1-2 minutes, stirring constantly.
Gradually whisk in the milk, ensuring no lumps form. Continue to stir and cook until the mixture thickens.
Reduce the heat to low, add the cheddar, mozzarella, and Parmesan cheeses, and stir until melted and smooth.
Season the cheese sauce with black pepper and salt.
Combine the cooked pasta with the cheese sauce in the saucepan, stirring to coat the pasta evenly.
Serve hot, garnished with additional cheese or herbs if desired.