Having suffered immense PTSD after the events of ANB, Spyro still has nightmares about his battle to the death with Cynder. But since no one gave a shit about him or his nightmares (or safety or well-being for that matter), He decided to sleep out on the balcony, exposing himself to all forms of danger. Luckily for him, Sparx wakes him up and tells him that Cynder couldn't take the molestation anymore and decided to run from the guardians. Spyro then sets out to stop her, because since when can females decide for themselves.
Cynder leaves anyway, Causing Spyro to trip on some acid. He starts to hallucinate about some old dragon who's surprisingly nice to Spyro considering his age. Since Spyro doesn't trust him, the dragon gives him command over time. He then identifies himself as the "Chronicler" and instead of telling Spyro what he must know, Or giving him a home address, Or even telling him what he looks like, He tells Spyro to look for a tree in the middle of a jungle. Spyro finally comes to and realizes that he's in a completely different location and that apes want him dead (again). He goes full serial killer and kills over 50 apes in the span of 15 minutes. The apes then realize they pissed off the wrong dragon and run away, King Arthur style.
Upon realizing that everyone's favorite sex toy has run away, The guardians and Spyro hold an emergency meeting to find her. Naturally, Ignitus sends everyone else to safe locations and Spyro to a haunted jungle, Effectively excluding himself from doing any work.
Upon arriving at said jungle, Spyro fucks up the wildlife by killing half its inhabitants including bugs, boars and flying jellyfish monsters. He then realizes there are pirates in the jungle for some reason. After killing an even bigger number of pirates, Spyro reaches the tree he saw in his nightmare. Unfortunately the tree was just a decoy meant to lure Spyro to his death, and a massive creature called "Arborick" attacks Spyro. Since Arborick was just a mindless creature whose only crime was being home, Spyro feels it needs extra punishment, and burns the wooden creature to death. After the creature dies, Some random pirates find Spyro and take him away to serve as gladiator and kill other creatures for their entertainment.
After killing two scorpions whose tails were in fact fully functioning cannons, Spyro is thrown against a literal flying shark ship that shot fire out of its "mouth". The ship was, of course, no match for his strength. Since the former two matches were clearly too safe, he is sent to the executioner and immediately shows him who does the executin' 'round here. Somehow the pirates had previously captured Cynder and pit the two baby dragons together. Luckily Gaul's forces finally got over their fear of Spyro, attack the fleet, and take Cynder for themselves. Spyro decides the best course of action to save Cynder is to spend an obscene amount of time in the pirate fleet instead of flying directly after Cynder.
After destroying well over 3 quarters of the fleet and their ships as well and flying to ship after ship, killing Gaul's forces as well, the fleet commanders realize they fucked with the wrong dragon, and decide to kill him. It only takes two minutes for Spyro to kick their asses hard. He gives them a five second headstart, and then follows to finish them off elsewhere. He finally kills the main pirate baddie by throwing him off a ramp into the purple sea below. Sparx finally does something useful and punches his parrot to death, and the two take off to continue their search for the Chronicler. Spyro's acid kicks in again in mid air and he falls to his watery grave. But luckily for him there was a giant turtle waiting directly below.
Spyro wakes up in Atlantis and realizes it's still inhabited by some random creatures. Naturally his first act is to wipe out the last of the Atlanteans. After spending an eternity in Atlantis and unlocking doors by pushing crystal spiders into the ground or pulling their legs off and putting their heads inside certain containers before killing them with his elemental powers, Spyro is told that he should face his greatest fear, which is fighting a dragon figure who's supposed to look like Cynder, but she ain't foolin' anyone. After killing the beast and effectively emptying Atlantis of life, Spyro finally meets the Chronicler and immediately trusts him. He tells Spyro that the whole mission was just meant to preserve Spyro for the upcoming apocalypse, but Spyro suggests they also preserve Cynder just in case they need to repopulate the earth. The Chronicler falls for this and tells Spyro that she's in Malefor's main base of operations, the well of souls. Our hero leaves for the mountain of Malefor immediately.
Upon reaching the mountain of Malefor, Spyro goes apeshit on the inhabitants and kills everything that moves (even the ghosts). He then gets in an argument with Gaul over who gets to keep Cynder. After negotiations go sour, the two sides decide to settle things with fist-i-cuffs, And engage in a fight in which Gaul gets his ass kicked. He forgets that Spyro has the ability to fly and destroys the floor they were standing on. Luckily for him Spyro actually forgets how to fly and both fighters fall unto another floor that was built for the sole purpose of an epic showdown 20 meters below. Needless to say they both survive. Spyro falls into a beam of pure convexity energy which kills everything in a matter of seconds. But he not only survives direct contact with said beam, He gains a new power and uses it to turn Gaul into stone, and then shatters the stone and puts the remains in a jar, pees in the jar, throws the mix into outer space and blows up the shuttle.
Spyro (with Cynder's help) then tells Malefor's essence to GTFO but the mountain starts crumbling for some reason. Suddenly Spyro realizes he has the power to encase everyone in some crystal for an untold amount of time without killing them due to lack of air, starvation and thirst, And does so without rethinking the consequences. Luckily for the trio, he's right and the crystal survives a literal mountain falling on it. Malefor is released to fuck with the world as he sees fit, but he makes sure to escape offscreen.
Of course, the story's not over yet and after the credits, It is revealed that a cheetah looking creature (whose identity is totally unknown to all Spyro fans) has somehow realized they were in the mountain of Malefor all along.