How Zexion joined the Tourney
Some time before Marluxia's official recruitment, Vexen tromped down the stairs of Twilight's View, calling out for Zexion and demanding to know where Xemnas was. Zexion answered that Xemnas was in the Chamber of Repose, and though Vexen complained, he decided to wait for Xemnas to return.
Xigbar was eavesdropping on the conversation, and dropped down after Vexen left. Zexion told him that he should continue his mission with Xaldin to recruit new members. After a short argument, Xigbar told Zexion that he had seen Xemnas, before they became Nobodies, conversing with someone in the underground laboratory. Even though no one was supposed to be there, Xigbar believed that it could be his other "friend". That friend is believed to be Aqua's armor which she sent with Terra-Xehanort.
Zexion is present when Xion joins Organization XIII. Zexion later teaches Roxas how to fill the mission gauge in Twilight Town before being sent away to Castle Oblivion. True to his personality, he was patient with the Keyblade wielder, carefully and calmly explaining the filling of the gauge in great detail.
After Axel returns from Castle Oblivion, Axel specifically mentions that he had eliminated Zexion during a conversation with Saïx. Sometime later, Axel admits that he doesn't mind "getting his hands dirty" to Saïx, and comments on killing both Zexion and Vexen.
During Xion's nightmare on Destiny Islands, Roxas stands on the beach of the island, missing his friend. He later sees the hooded Xion and approaches her. She removes her hood and turns out to be none other than Zexion, who proceeds to taunt a younger version of Riku as he did in Kingdom Hearts: Chain of Memories. The scene then begins to fade, Xion (in the form of the shocked Roxas) undergoing a series of transformations until she finally takes Sora's form for the first time.
After Sora had been lured into Castle Oblivion, Zexion discovers two other scents deep in the dungeons of the castle. One of them belongs to a Maleficent formed from someone's memory, having been given life by Castle Oblivion's unique properties. Originally, he mistakes the other scent to be that of "The Superior". Eventually, however, Zexion and his cohorts determine that the scent belongs to Riku, who had appeared in the castle by force of will after Sora's arrival. Vexen hypothesizes that the darkness in Riku's heart, "Ansem", caused Zexion to mistake him for "the Superior", calling the effect "fascinating." Specifically, Riku's heart is plagued by the presence of Ansem.
Zexion, as well as Lexaeus and Vexen, come to see that Marluxia, keeper of Castle Oblivion, intends to take control of Organization XIII, with the help of Larxene, by using Sora as their puppet. Though they see that they can use Riku to counter Sora, they decide to oppose Marluxia's plot by having Vexen investigate Marluxia under the guise of offering to help using the Riku Replica he creates with combat data from the real Riku. However, Vexen is eventually killed on Marluxia's orders by Axel, whom Zexion and Lexaeus had been unsure about trusting. Axel later tells them he had performed the deed only to gain Marluxia's trust, and continues to cooperate with Zexion in tracking Sora and Riku.
Seeing that Vexen's efforts to derail Marluxia's plan had failed, Zexion sends Lexaeus to sway Riku into joining them, but Riku refuses to allow darkness to control him and defeats Lexaeus in combat. With the last of his strength, Lexaeus manages to knock Riku unconscious, rendering him helpless. However, before he can finish the job, Ansem takes control of Riku's body and finishes Lexaeus with the power of darkness. Riku is then enveloped in his own personal darkness, where "Ansem" tries to corrupt him—however, he is saved by King Mickey and continues ascending Castle Oblivion.
After Lexaeus dies in his failed attempt to subvert Riku's resistance to darkness, Zexion discusses the Organization's fate with Axel and learns that Larxene has been killed as well, bringing the number of Organization members eliminated to three. Axel tells him that he himself was defeated by Sora as well, and that Marluxia is almost certainly the next to go. Zexion decides that with the possibility of Marluxia dying soon, Riku is no longer needed, and heads off to intercept him.
Zexion appears before Riku while he is between floors of the castle, shortly after the death of Marluxia. As the force of Marluxia's death shakes the castle, Riku halts with surprise and comments how a very strong scent in the air has died. Zexion materializes in front of him and tells him that Sora has just defeated Marluxia. Riku is surprised to learn that Sora is also in the castle, but Zexion tells him he would never be able to face him after having such darkness in his heart.
He gives Riku a World Card to Destiny Islands. While he explores it, Zexion reappears, and continues to play on his guilt, telling him Sora will always oppose him as a host of the dark. Zexion vanishes and Riku winds up facing a Darkside Heartless. After he defeats it, Sora then appears himself, brandishing his Keyblade and accusing Riku of being corrupt. He envelops Riku in light, rendering him unable to do anything. Instead of drowning Riku into helplessness, however, the predicament causes Naminé to come to his aid. In the guise of Kairi she tells him that he should stop rejecting the darkness within his heart, and instead draw on that power to free himself of the oppressing light and strike out at Sora.
He wounds Sora, whose disguise falters to reveal Zexion, who had been using his powers of illusion to deceive Riku. Zexion is astounded by Riku's ability to control the darkness, and is also enraged at his perseverance. He decides to engage Riku in combat himself, albeit wounded, but still puts up a rather difficult fight. However, Riku eventually overcomes and defeats Zexion.
After escaping from Riku, Zexion appears in the meeting room he shared with Lexaeus and Vexen, flabbergasted as to how Riku can wear darkness the way he does as no one has ever done so before. Waiting for him are Axel and a companion. In a panic, Zexion thinks Axel's companion is Riku himself, but then realizes it's only Riku Replica. Axel and the replica then approach Zexion, and Axel directs the replica's attention to his lack of wholeness. He tells him that if he can find strength that the real Riku doesn't have, he can become a whole person of his own, rather than a mere puppet or whole copy of Riku.
Axel then suggests that he should start by eliminating Zexion and taking his powers for himself. Zexion is horrified by Axel's suggestion and tells him he can't do that, but before he can do anything, the replica absorbs Zexion's life force, taking his power; judging by Axel's line of Zexion finding out "way too much", Axel having purposefully set this up in order to move Saïx up within the ranks of the Organization.
Returned to life, Zexion sets out to conquer the Furchester Hotel. He first finds the proprietor, Funella Furchester holding a party for her nephew Elmo.
Character Select Screen Animation
Prepares to open his lexicon book, the Book of Retribution.
After the announcer calls his name
Opens the Book of Retribution and summons illusions as the camera zooms then says "You should share your powers!"
Magnet Snatch (Neutral)
Zexion creates a sphere of Magnet energy in one of his Books of Retribution, sending it at the opponent to steal his/her Neutral special attack.
Soul Eater (Side)
Zexion summons two clones of himself to fight for him for thirteen seconds.
Dark Revenge (Up)
Zexion sends a clone to attack the opponent with its Soul Eater, while he flies into the air does a downward slam attack.
Cyclone Snatch (Down)
Zexion creates a damaging black vortex as he says "Your memories shall be mine!" in the center of battlefield that draws the opponent in and steals two Special Attacks from the him/her if too close.
Catastrophe (Hyper Smash)
Zexion and his body clones create a sphere of energy saying "See my illusion!" in the center of the battlefield, rotating around and shooting beams of energy at it. The sphere will then burst into a wave of unavoidable light energy.
Meteor Mirage (Final Smash)
Zexion and his open lexicon are brought into the air as he says "You think you can be forgiven?!". While in the air, Zexion summons many balls of dark indigo energy to bomb the field, dealing a large amount of damage to enemies hit by the barrage.
- Zexion closes the Book of Retribution and says "You brought it upon yourself!"
- Zexion summons a dark vortex and says "everything that is you. is now mine."
- Zexion summons three copies of himself and then push their hands out, then the real Zexion says "If you only understood my power."
Zexion flies down and readies the Book of Retribution saying "This is absurd. Then I shall make you see... That your hopes are nothing. Nothing but a mere illusion!"
- Zexion's rival is the main proprietor of the Furchester Hotel and Elmo's aunt, Funella Furchester.
- Zexion shares his Japanese voice actor with Gaara, Pip of the Pip and pop duo and Robbie Rotten.
- Zexion shares his German voice actor with Dangoro, Ermac, Piandao, Katsuie Shibata, Toriko and Mr. Peabody.
- Zexion shares his Arabic voice actor with Blondie, Magnus, Vincenzo "Vinny" Santorini and Bryce Adams.