In his teenage years Clive serves as Joshua's bodyguard, blessed with some power from the fire Eikon Phoenix, and lives with his parents with Jill as their ward. The brothers accompany their father, Duke Elwin, to a ceremony to awaken Joshua's powers when they are ambushed by Sanbreque soldiers. Elwin's death triggers Joshua's destructive awakening as the Phoenix, and an Eikon named Ifrit emerges moments later and kills the Phoenix, with Clive swearing revenge. Clive's mother Anabella, who despises Clive's lack of blessing and betrayed Rosaria to preserve her bloodline, has him enslaved as a magical soldier in Sanbreque's army. Thirteen years later, Clive is sent behind enemy lines during a fight between the Dhalmekian Republic and the Iron Kingdom to assassinate the latter's Dominant, revealed to be an enslaved Jill. He deserts to free her, and the two are rescued by Cid, who agrees to help Clive search for Ifrit's Dominant. Tracking word of an unknown Dominant, they fight Benedikta, from whom Clive takes the power of her Eikon Garuda. A disturbed Benedikta is then attacked by bandits and transforms into a raging Garuda, which in turn triggers Clive to transform into Ifrit and kill her. While Clive briefly despairs at the fact that he is Ifrit and the one who killed Joshua, Cid encourages him to keep searching for the truth behind his transformation.
After Clive and Jill see the full oppression inflicted on Bearers and their sympathizers in occupied Rosaria, they join Cid in a quest to destroy the nations' Mothercrystals, which are causing the Blight by draining aether from the land. They infiltrate Sanbreque's capital but encounter a monster within the Mothercrystal that mortally wounds Cid before the Mothercrystal is destroyed. The monster is part of an otherworldly being called Ultima, which attempts to possess Clive. Joshua, who survived Ifrit's attack due to the Phoenix's powers, stops and contains Ultima within himself. Hugo, who was in love with Benedikta, is manipulated by Barnabas's agents into believing Cid is responsible for her death. Five years later, Clive, now using the title of "Cid" and carrying on Cid's mission, uses the war between Sanbreque and the Dhalmekian Republic over the occupied Crystalline Dominion as a cover to destroy the Iron Kingdom's Mothercrystal. Ultima continues working through the worshipping Barnabas and the form of Olivier, Anabella's son by Sanbreque's emperor. Clive later fights Hugo and reveals to him that he killed Benedikta; desperate for revenge, Hugo transforms into a raging Titan. Having gained full control of Ifrit, Clive kills Hugo and destroys the Dhalmekian Mothercrystal.
Under Joshua's advice, Dion stages a coup against Anabella but in the process accidentally kills his father and transforms into a raging Bahamut. Clive destroys the Dominion's Mothercrystal and reunites with Joshua, helping him defeat Bahamut. Dion survives and kills Olivier, causing an unhinged Anabella to kill herself. Clive then moves against Barnabas, killing him and destroying Waloed's Mothercrystal, but Ultima reveals this to be part of his plan to shape Clive into a vessel for him to inhabit through Clive absorbing Eikons. Joshua's research reveals that Ultima's people seeded Valisthea with the Mothercrystals to siphon aether for a powerful resurrection spell after succumbing to an earlier Blight, creating humans to breed a vessel powerful enough to cast it. Clive, Joshua, and Dion mount an attack on Ultima's sky fortress of Origin, where Ultima's fragments merge to complete their plan. Dion is killed, and Joshua left mortally wounded after the Ultima fragment is forcefully removed. Joshua sacrifices himself to give Clive his Eikon. After killing Ultima, Clive heals Joshua's wounds and destroys the final Mothercrystal within Origin to remove magic from Valisthea. A post-credits scene in Valisthea's future, where magic is considered a myth, shows a family living in peace.