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Whilst the other endings in Shadow The Hedgehog: Flames Of A Black Moon are simply assumptions of an ending and therefore cannot be considered canon, the True Epilogue can be unlocked after beating all 14 endings in the game. This story can also be unlocked by completing Expert Mode, which can be achieved by completing every mission of every act of every stage with an A or S rank.
In a brief cinematic (One that plays in every story prior to this one being unlocked), Shadow compliments the player for observing the stories that many people wrote about him. He says that he has decided that the player has earnt the final story.
Shadow had returned from an intensive training retreat on his Shadow Glider and arrives to Westopolis, a Metropolian city heavily influenced by Brooklyn and Chicago, and is one of three Boroughs of Empire City. Once he had returned, he witnessed from building view that small portions of the city was in shambles. After overhearing police investigators of GUN discussing the cause of the incident, Shadow realizes that he has been framed for a terrorist attack on the city and GUN is holding a ransom on his arrest. A female officer named Topaz, however, saw Shadow, and the police commenced attacking him. But Shadow's knife sharp reflexes managed to save him. Shadow tried to reason with the forces, but they began attacking him nevertheless. Shadow then decided that enough was enough and, in an act of defense, fought back mercilessly. As reinforces arrived, Shadow continued to fight. Whilst fighting, a talisman deep inside the hedgehog's body, beyond the immortal's soul, began to glow, and Shadow threw a fireball at a truck, bursting the vehicle to flames. Shadow was amazed by his pyrokinetic ability, but before he could do any further, he was greeted by more reinforces. Shadow then escaped swiftly.
Later, in Westopolis gardens, an oriental themed park, Shadow read a newspaper on the story. Coming to the conclusion that he was framed, Shadow grows very frustrated, and then, very agitated. As if on cue, a crimson cloud overshadows the city and warships emerge from those clouds. Large, extraterrestrial warriors begin terrorising the streets. Shadow decided to help them, but one of the alien jets land in front of him, and out comes the pilot, who is one of the aliens. He claims himself to be Black Claw, a pilot of the Black Arms, implying that the aliens attacking are the Black Arms. He was sent by the High Priests (The Black Arms' military and political council) and a mysterious figure known as "The Leader" to get Shadow to assist their conquest. At first Shadow declined, wanting nothing to do with the war, but Claw said that Shadow shouldn't bother saving the humans as they don't show gratitude for his assistance and just treat him like a ghost. If Shadow works with them, then he shall be seen as a god, and learn of who framed him.
He then goes into Downtown Westopolis, a hybrid of Death City Acts 1-3(Westopolis, Lethal Highway and Cataclysm Border) and was assigned to fight off the human resistance, but instead went to find the Chaos Emerald in the area. Claw was angry at Shadow for his disobidience and threatened to strand him the far side of space if he was to disobey him again. Shadow questioned as to why he should do things his way, but Claw retaliated, saying that he has to work for royalty and he also said, "Yesterday, you were an outcast. Tomorrow you are a god, but today, you are my pawn". So Shadow agrees to listen to his orders.