Prep the pan and oven. Heat the oven to 325°F (165°C).
Line the bottom of a 9-inch springform pan with parchment and lightly grease the sides.
Make the crust. Stir crushed cookies, almond flour, cocoa, sweetener, salt, and melted butter until the mixture looks like damp sand. Press firmly into the bottom of the pan. Use a flat-bottomed cup to compact it evenly.
Parbake the crust. Bake for 8–10 minutes until set and fragrant.
Cool on a rack while you make the filling.
Beat the cream cheese. In a large bowl, beat cream cheese on medium speed until smooth and lump-free, about 1–2 minutes. Scrape the bowl.
Add yogurt and sweeteners. Mix in Greek yogurt, sugar or sweetener, vanilla, salt, cocoa powder, and protein powder on low speed until combined. Avoid whipping too much air.
Add eggs. Beat in eggs one at a time on low, scraping the bowl between each.
Stop mixing as soon as the batter looks uniform and glossy.
Swirl in chocolate. Drizzle the melted, cooled dark chocolate into the batter. Fold gently 3–4 times for a marbled effect, or mix fully for a deeper chocolate color.
Prepare a gentle bake. Wrap the outside of the springform pan with two layers of foil to protect from water. Place the pan in a larger roasting pan.
Boil a kettle of water.
Fill and bake. Pour the batter over the crust. Set the roasting pan on the middle rack and pour hot water around the cheesecake to reach halfway up the sides. Bake 45–55 minutes, until edges are set and the center jiggles like set Jell-O.
Cool gradually. Turn off the oven, crack the door, and let the cheesecake rest inside for 45 minutes.
Then move it to a rack and cool to room temperature.
Chill to set. Cover and refrigerate at least 6 hours, preferably overnight, for the best texture and clean slices.
Make the topping. Warm the milk until steaming, then pour over chopped chocolate with coconut oil and a pinch of salt. Let sit 1 minute, then stir until smooth and glossy.
Finish the cake. Release the chilled cheesecake from the pan. Spread the chocolate topping over the surface, letting it gently reach the edges.
Chill 20–30 minutes to set. Garnish as you like.
Slice cleanly. Use a hot, dry knife for neat slices. Wipe between cuts.