The game begins inside a temple, where a large red dragon named Ignitus is watching over an egg; it is the "Year of the Dragon", a time every ten generations when new dragon eggs are brought to the realm. A dragons' prophecy tells that every ten generations, a rare purple dragon will be born, who will direct the fate of that era; Ignitus is looking after such an egg.
The dragons are, however, at war with an enemy known as the "Dark Master" who also knows of the prophecy, and lays siege to the temple, intent on destroying the brood of eggs. Ignitus escapes with the purple dragon's egg, leaving it to drift downriver into a swamp, hoping for the best. The egg is discovered by a family of dragonflies, and upon hatching, they name the dragon Spyro and adopt him into the family and raise him as one of their own, alongside Sparx, a young dragonfly born the same day.
One day, after coming under attack by strange foes and discovering that he can breathe fire, Spyro is told that he is not a dragonfly himself but a stranger from a distant land; Spyro decides to leave the swamp in search of his true home; Sparx, though reluctant at first, decides to follow along. Spyro is pursued by hostile forces, but eventually comes into contact with a distraught Ignitus, who although pleased that Spyro is alive, fears that with the Dragon Temple under occupation by their enemy, and led by an enemy dragon named Cynder, their war is already lost.
Spyro convinces Ignitus to lead him to the Temple, and is able to drive Cynder's forces out, after which Ignitus tells Spyro more about their war against the dark armies, offers Spyro some training in the art of the fire element, and then sends Spyro off to rescue three other dragons from Cynder's forces. One by one, Spyro clashes with Cynder's armies, rescues the three other dragons, Volteer, Cyril, and Terrador, while acquiring new skills and training along the way. It is learned that Cynder has been draining the dragons' power into crystals.
Cynder, however, attacks Spyro shortly after he rescues the final Dragon Guardian, Terrador; Ignitus intervenes to fight Cynder but is captured. It is revealed that it was the four dragons who originally sealed away the Dark Master, and that Cynder is using the dragons' drained powers to open the seal. Ignitus's power is the final key in unsealing the Dark Master, so Spyro is sent on a final, direct assault against Cynder's fortress.
Spyro attempts to fight Cynder, but Cynder succeeds in draining Ignitus's power of fire into a crystal, and escapes to the sealed realm of the Dark Master. During the fight, Spyro had noticed there was something familiar in Cynder's eyes. Ignitus then tells Spyro the rest of the story of what happened the night of the attack on the temple. After sending Spyro's egg down the river, Ignitus had returned to see that the Dark Master's forces had destroyed the brood of eggs, except one - for only a dragon born in the Year of the Dragon can open the portal and release the Dark Master: Cynder, who had been transformed by the Dark Master's sinister powers.
Ignitus fears that it is too late to stop her, but Spyro pursues Cynder and forces a showdown, eventually using all of his power in a final attack which defeats her, purging her of the Dark Master's influence and returning her to her true form, a young dragon the same size as Spyro. The realm begins to collapse in on itself; Sparx insists on making a quick exit but Spyro declares he will not leave Cynder behind with the Dark Master; though barely, Spyro is able to grab Cynder and escape safely.
Though victorious, the battle cost Spyro much of his own strength and powers, and both Spyro and Cynder suspect that the Dark Master is still alive somewhere; the war is still not over.
SourceThe story begins with Spyro following Cynder through the jungle surrounding the Dragon Temple. Spyro catches up with her and asks her not to leave. Cynder then leaves saying that she's sorry for what she has done in the previous game. Cynder runs off, leaving Sparx and Spyro alone. Soon after she is gone, the Temple is attacked by an army of apes. After Spyro repels the attack, Ignitus, the leader of the dragons and master of fire, sends Spyro to seek out a tree that Spyro saw in a vision (that in his dream, he gets his powers back, as he lost them at the end in The Legend of Spyro: A New Beginning) while Ignitus looks for help against the Apes. As Spyro searches for the tree, he also searches for another dragon known as the Chronicler, who asked Spyro in a vision to find him. After he finds the tree, Spyro is captured by pirates, and is taken onboard their ship to take part in gladiatorial combat.
After Spyro escapes the pirate ships, he discovers that the Apes have established a base on the Mountain of Malefor, also known as the Well Of Souls, in an effort to revive the Dark Master using a lunar alignment called the Night of Eternal Darkness. He also discovers that they are keeping Cynder prisoner hoping to turn her to their side.
Spyro eventually finds the Chronicler, who tells him about the Dark Master. According to him, the Dark Master was the first purple dragon; his raw power allowed him to master practically every elemental power. When his growth failed to stop, he was exiled and sealed away by the dragon elders, but not before he taught the Apes how to use dragon magic. The Chronicler wants Spyro to hide from the Apes until a later time, but Spyro insists on going to Cynder’s aid.
When he gets to the mountain, Gaul, the Ape King, orders Cynder to attack Spyro. When she attacks Gaul instead, he knocks her out and challenges Spyro himself. During the fight, the lunar alignment occurs, and the evil energy it generates is channeled through Spyro. He uses his immense power to kill Gaul, and then leaps back into the beam of evil energy. Cynder awakens and knocks Spyro out of the beam, freeing him from the beam's power. When the alignment passes, the mountain begins to crumble around Spyro, Sparx and Cynder. Remembering the Chronicler's words about riding out the storm, Spyro uses his powers to encase himself, Cynder and Sparx in crystal to protect them as the Well of Souls collapses.
SourceThe game begins with Spyro and Cynder being broken free of their crystalline prison by mysterious enemies. Spyro and Cynder are bound together with mysterious green energy chains created by the Dark Master, and carried away as Sparx is found by Hunter of Avalar, who was watching them from the shadows. Meanwhile, Spyro and Cynder find themselves in a dark, volcano like area. When they try to leave the area, they cannot as they are chained to the platform they awoke on. After several waves of enemies and avoiding a earth monster called the Golem that attacks them soon after, they manage to escape with the help of Hunter, who is with Sparx. He explains the situation to them after they leave the Catacombs, and he shows them what the Dark Master has done since his escape from the Well of Souls during the Night of Eternal Darkness.
Once they reach the Dragon City of Warfang, the dragons and Hunter are separated as the city is under siege by Malefor's forces. After a long and fierce battle that ends in the siege being defeated, Spyro, Cynder, and the Dragon Guardians are reunited. But the victory is short lived as the Golem returns and uses parts of the city to create a new arm (He lost his arm in the catacombs). Spyro and Cynder defeat the Golem by destroying the Dark Crystal in it's head. Later that night, the Dark Master, Malefor, sends them a message. He has revived the Destroyer, an ancient creature whose only purpose is to renew the world by bringing about its destruction. As they will be unable to catch up with the creature if they fly after it, Ignitus and Cynder hatch the plan that going underground is the only way to catch up with it in time.
Cynder and Spyro manage to open the gates to the underground Ruins of Warfang, which leads the attack forces to the canyon where the Destroyer will complete the Ring of Fire. By destroying a nearby dam, they manage to stall the Destroyer long enough to destroy its Dark Crystal heart, but it was an effort spent in vain. The Destroyer manages to complete the Ring of Fire, and Ignitus orders everyone underground as he escorts Spyro and Cynder to the Ring of Fire. In order to get them to the Burned Lands, which will lead them to Malefor's Domain, Ignitus sacrifices himself in the crossing and Spyro, overcome with grief, tries to go back to find him, but is stopped by Cynder.
After getting through the Burned Lands and Floating Islands, they arrive at Malefor's Domain and confront him. He taunts Spyro by telling him that the destiny of all purple dragons is to bring about the world's destruction.After a long series of battles against Malefor, they reach the heart of the world. Malefor is defeated by the combined efforts of Spyro, and Cynder, and is sealed away by the spirits of the Ancestors, but the world is still falling apart. Ignitus' spirit gives Spyro hope. Spyro tells Cynder to flee while he stops the catastrophe, but she refuses to leave him. As Spyro unleashes a powerful Fury wave, Cynder whispers "I love you". Spyro's magic restores the planet.
After the credits, the Chronicler says that a new era has come and with each new era, a new Chronicler is chosen to record the triumphs and failures of that era. He welcomes Ignitus, who is revealed to have lived, to take his place. Before passing his mantle, the Chronicler informs Ignitus that though he has tried his best, he cannot find Spyro and Cynder in the book that details dragons that have died. As Ignitus becomes the new Chronicler, he wonders where Spyro could be. The last scene of the game is Spyro and Cynder flying though a meadow in Avalar, having escaped from the world's core and finally earned their happy ending.
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