The Golden Spider reveals himself to be Chakravartin, and refers to Asura as the Redeemer. Chakravartin states that he himself unleashed the Gohma to test the inhabitants of Gaea, in the hope of finding a successor and ending his need to watch over Gaea. Asura attacks Charkravartin only to find himself outmatched, even while in Mantra form. Asura unleashes his Wrath form in hopes of saving an imprisoned Mithra, but to prevent his destruction, she sends him falling down to Gaea along with Yasha. Chakravartin proclaims the world a failure and prepares to cleanse and remake it once more, which will kill the surviving demigods and humans. He seizes the Karma Fortress for the cleansing and detaches the Brahmastra, causing it to crash down to Gaea. Awakening on the surface, Yasha realizes that the still-unconscious Asura is the only one who can save the planet. Yasha defends him from surviving Gohma, then installs the Mantra Reactor from the Brahmastra into Asura. The reactor will prevent Asura from destroying himself in the final battle, and can augment his powers to stand against Chakravartin. Yasha removes his own mantra core to revive Asura, and prepares to battle him as a catalyst for Asura's new potential.
Asura wakes up to find Yasha eager to battle. Though confused, Asura accepts. His new mantra core comes online during the fight, causing him to critically injure Yasha. As Asura prepares to land the final blow, he realizes what Yasha has done for him and stops the fight. Yasha is already beyond help, and dies with a smile on his face. Before departing, Asura admits he had always considered Yasha as a brother rather than an enemy.
Preparing for his final confrontation, Asura meditates and sees visions of the other Deities and Durga, reminding him of his purpose. He heads into space to confront Chakravartin. Chakravartin fires the doomsday blast at Gaea, but Asura transforms into a near-godly form called Asura the Destructor and deflects it. Asura engages Chakravartin, who again requests that Asura become the new god of the planet only to be rejected once again. The very fabric of time and space begins to come apart as they duel for the fate of Creation. Chakravartin is eventually pressed into his final form, but is brought to his knees by Asura's sheer force of will. As Asura prepares to kill Chakravartin, Mithra breaks free and urges him to stop. Mithra states that if Chakravartin is killed, all mantra will cease to function. This will render all of Shinkoku's technology and the powers of the demigods useless, including those keeping Asura alive. Asura chooses to destroy Chakravartin nonetheless, resigned to his fate and happy to die so long as Mithra can live free from danger. As the landscape around him collapses, Asura shares his final words with Mithra and vanishes, free of his wrath for the first time.
Mithra is sent back to Gaea, where she integrates with the surviving humans. She spends many years recounting the tales of her father to the flourishing mortal children on Gaea before presumably passing away peacefully of old age.
In the epilogue, It becomes apparent to the player that the events of Asura's Wrath actually occurred in the far distant past. The demigods reverted to humans after Chakravartin's demise, their exploits and very existence forgotten to modern society. Indeed, the truth about humanity's origins and near-extinction lives on only in vague stories passed down from prior generations.
The cycle of reincarnation is shown to have continued despite Chakravartin's absence, and all of the Deities including Asura have been reborn on present day Earth. A series of still frames shows Asura blissfully spending time with his reincarnated family, unaware of his past life's exploits. Suddenly, a giant meteor appears in the sky, presumably a new threat. Feeling a strangely familiar urge to defend the helpless, Asura stands prepared for battle.