In 1482 Mobotropolis, a Mobian cat puppeteer narrates the origin of the titular Werehog twenty years prior. In 1462, a group of outsiders sneak illegally into Mobotropolis but are ambushed by Dr. Julian Robotnik, Mobotropolis Minister of Science, and his soldiers. A Mobian hedgehog woman in the group attempts to flee with her Werehog baby, but Robotnik chases and kills her outside of Mobotropolis. He tries to kill the baby as well, but the captain intervenes and accuses Robotnik of murdering an innocent Mobian female hedgehog. To atone his sin, Robotnik reluctantly agrees to raise the Werehog child in Notre Dame as his son, naming him "Sonic."
Twenty years later, back in 1482, Sonic develops into a kind yet isolated young blue hedgehog, though still a Werehog who has lived inside the cathedral his entire life. A trio of living Mobian-Tails, Knuckles, and Shadow-serve as Sonic's only company and encourage him to attend the annual-held Mobian Festival. Despite Robotnik's warnings that he would be shunned for his deformity, Sonic attends the festival and is celebrated for his awkward appearance, only to be humiliated by the crowd after two of Robotnik's guards start a riot. Robotnik refuses to help Sonic, but Blaze, a kind Mobian female purple cat, intervenes be freeing the Werehog and uses a trick to evade arrest. Robotnik confronts Sonic and sends him back inside the cathedral.
Blaze follows Sonic inside, only to be followed be Captain Silver of Robotnik's guard. Silver refuses to arrest her and instead tells Robotnik that she has claimed asylum inside the church; the archdeacon orders Robotnik and his men out. Blaze finds and befriends Sonic, who helps her escape Mobotropolis out of gratitude for defending him. She entrusts Sonic, a pendant containing a map to the hideout, the Court of Miracles. Silver soon develops lustful feelings for Blaze and, upon realizing them, begs the Chaos to save him from her "spell" to avoid eternal damnation. When Robotnik discovers that she escaped, he instigates a search for her, which involves arresting outsiders and setting fire to countless houses in his way. Horrified when Robotnik orders him to burn down a house with a family inside, Silver is struck by an arrow and falls into the River Seine, but Blaze rescues him and takes him to Mobotropolis for refuge. The Mobians encourage Sonic to confess his feelings for Blaze, but he is heartbroken to discover she and Silver have fallen in love.
Robotnik returns to Mobotropolis later that night and discovers that Sonic helped Blaze escape. He bluffs to Sonic, saying that he knows about the Court of Miraciand intends to attack at dawn with 1,000 men. Using the map Blaze gave him, Sonic and Silver find the court to warn outsiders, only for Robotnik to follow them and capture all the outsiders present.
Robotnik prepares to burn Blaze at the stake after rejecting his advances, but Sonic rescues her and brings her to the cathedral. Silver releases the outsiders and rallies the Mobian citizens against Robotnik and his men, who try to break into the cathedral. Sonic and his friends pour molten lead onto the streets to ensure no one enters, but Robotnik successfully manages to get inside. He pursues Sonic and Blaze to the balcony where he and Sonic fight, and both fall over the edge. Afterward, Sonic accepts that Silver and Blaze are in love, and he gives them his blessing. The two encourage him to leave the cathedral into the outside world, where the citizens hail him as a hero and accept him into society.
