Preheat the oven to 350°F/180°C and line a 9-inch springform pan with parchment paper. Wrap the bottom of the pan with aluminum foil to prevent leaks.
Melt bittersweet chocolate and butter in the microwave in a heatproof bowl, mixing every 30 seconds until completely melted. Let cool slightly.
With a hand mixer, beat granulated sugar, eggs, and vanilla extract together on medium high speed until frothy and pale.
While beating, pour the melted chocolate and butter mixture in. Continue mixing until well combined.
Fold the all purpose flour, cocoa powder, and salt into the wet ingredients until the dry streaks disappear.
Pour the batter into the prepared pan and bake for 25-30 minutes or until a toothpick inserted in the center comes out clean. Remove from the oven and let cool while you make the cheesecake batter.
Reduce the oven heat to 325°F/165°C. Fill a large oven safe skillet or casserole with warm water and carefully place it on the bottom rack. This is the water bath.
Melt the semi-sweet chocolate chips in a large bowl in the microwave. Stir every 30 seconds until completely melted. Set aside to cool slightly.
Beat the cream cheese and sugar together in a large mixing bowl with a mixer until smooth. Scrape down the sides of the bowl with a rubber spatula.
Pour in the melted chocolate chips and beat in the vanilla, cocoa powder, and salt on low until smooth and creamy. Beat in the sour cream.
Mix in the eggs one at a time, scraping the sides of the bowl after eggs 2 and 3.
Pour the filling over the crust and smooth out the top. Place in the oven directly above the water bath and bake for 60-70 minutes. It's done when the edges are set and the center jiggles like Jell-O.
Turn off the oven, crack the door open, and let the cheesecake cool inside for 1 hour. Remove from the oven and cool on top of it for 1 more hour before covering in plastic and chilling in the refrigerator overnight.
Add chocolate chips to a large bowl. Microwave heavy cream in a separate container for 45 seconds. Pour over the chocolate and let sit for 1 minute.
Whisk the chocolate and cream together until smooth and glossy. Place plastic wrap over the surface and chill in the refrigerator for an hour.
Once the cheesecake and ganache are both cool, release the springform pan and remove the cheesecake. Spread ganache over the top and add candy coated chips. Slice and enjoy!