Preheat oven to 300 degrees and boil some water in a kettle for later.
To prepare crust; In a small bowl, combine graham cracker crumbs and brown sugar. Add melted butter, stirring to combine. Press crust into bottom of a 9-inch springform pan. Bake for 6 minutes, remove and let cool.
To prepare the chocolate layer, in a medium bowl, combine chocolate and butter. Microwave on high in 30 second intervals, stirring after each, until chocolate is melted and smooth (about 2 minutes total).
Whisk in sugar, eggs, and flour, until combined. Pour into bottom of cooled crust, and bake for 15 minutes. Remove and let cool completely.
To prepare peanut butter layer, in a large bowl, beat cream cheese and brown sugar at medium speed with an electric mixer until creamy. Beat in peanut butter until combined. Add in eggs and egg yolk, one at a time, beating well after each addition. Stir in the heavy cream. Pour over cooled chocolate layer.
Wrap foil around the springform pan and place the pan in a larger roasting pan. Pour boiling water halfway up to the springform pan. Kind of like when you’re baking a soufflé.
Bake for 1 hour, until the top of the cheesecake is brown. Turn the oven off, prop the door open with a wooden spoon and let the cheesecake sit in there for another hour.
To prepare chocolate ganache, in a small bowl, combine chocolate and cream. Microwave on High in 30 second intervals, stirring after each, until chocolate is melted and smooth (about 1 minute total). Spread over cooled cheesecake. Garnish with chopped chocolate Reese’s Peanut Butter Cups and enjoy!