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1 (9-oz.) box chocolate wafer cookies, broken into pieces
2 oz. bittersweet (not unsweetened) or semisweet chocolate, coarsely chopped
5 tbsp. unsalted butter, melted
4 (8-oz.) packages cream cheese, room temperature
1 1/2 cups sugar
3 tbsp. flour
4 large eggs
1 tbsp. grated orange peel
1 tsp. vanilla extract
1 cup pomegranate juice (see note)
3/4 cup sugar
3 tbsp. cornstarch
1 tsp. grated orange peel
1/4 cup fresh pomegranate seeds, for garnish
For crust: Preheat oven to 125 degrees. Finely grind cookies and chocolate in a food processor. Add butter and blend until clumps form. Dump the crumb mixture into the bottom of a 9-inch springform pan with 2 3/4-inch sides. Wrap your hand with plastic wrap and use your wrapped hand to press the crumb mixture onto the bottom and about 1 1/2 inches up the sides of the pan. Bake until set, about 8 minutes. Cool completely.
For filling: Increase oven temperature to 350 degrees. Wrap 2 layers of heavy-duty foil around the bottom and up the sides of the springform pan. Using an electric mixer, beat cream cheese and sugar in a large bowl until light. Beat in flour. Beat in eggs, 1 at a time, just until blended. Beat in orange peel and vanilla.
Pour filling into crust. Place springform pan in a large roasting pan. Fill roasting pan with enough hot water to come halfway up the sides of the springform pan. Bake until filling is just set in the center but still moves slightly, about 55 minutes. Remove cake from water bath; transfer to a rack and cool completely, about 4 hours. Refrigerate.
For topping: Combine pomegranate juice, sugar, cornstarch, salt and orange peel in a small saucepan. Cook over low heat, stirring constantly until the mixture comes to a boil. Continue cooking until the mixture is thick and clear. Cool to room temperature. Spread over the top of the chilled cheesecake filling. Sprinkle with fresh pomegranate seeds for garnish. Chill until set, about 1 hour.