Preheat oven to 350 degrees F. Grease an 8 or 9-inch pie dish with shortening.
Add the butter and the semi-sweet chocolate chips to a medium saucepan. Over medium heat heat the butter and chips until they are melted together and smooth. Stirring frequently.
Add the 1 cup of sugar and stir until the sugar is blended in. Add the two eggs one at a time, mixing just until they are stirred in. Fold in the flour until mixed in.
Pour the batter into the prepared pie pan. Place the pie dish into the preheated oven and bake for 15 minutes.
While the brownie bottom is in the oven, prepare the cream cheese topping.
Place the cream cheese in a medium bowl and beat with an electric mixer for about 30 seconds or until lightly fluffy. Add the 1/4 cup sugar and mix it in.
Add the egg and mix just until the egg is mixed in. Mix in the vanilla. Fold in the mini chocolate chips.
Once the brownie bottom is done remove from the oven. Spread the cream cheese topping over top the brownie bottom, being careful not to tear the top of the brownies.
Place back into the oven and bake for another 20 to 25 minutes or until the top of the cream cheese starts to brown.
Remove from the oven and set on a cooling rack for about 30 minutes.
While the pie is cooling make the chocolate ganache. In a small saucepan add the 1/2 cup of cream and bring to a simmer
When the cream comes to a simmer remove it from the heat and add the 1/2 cup of milk chocolate chips. Cover and let sit for 2 to 3 minutes.
When the 2 or 3 minutes is done stir the cream and chips until the mixture is smooth. Drizzle the chocolate over the cool pie.
Cool the pie completely before serving.