STORY MODEAxel's role in the beginning of the story is to bring Roxas back to the Organization. He wants to rescue Roxas from Diz and Ansem in order to save him from his new fate. Roxas doesn't know how to respond to Axel coming at him. Roxas asked for an explanation on who he is and why he is talking to him. Axel is disappointed but not startled to see that Roxas infact does not remember him. Roxas was bothered with the question why he has a Keyblade and subconsciously seeking out Sora, Roxas leaves the Organization. Axel, who found companionship in Roxas, is distraught by this decision. Shortly afterward, Roxas is captured by Riku and put in DiZ's Digital Twilight Town where his memory is wiped and replaced with an artificial one, leading him to believe he is a normal teenager. Axel is sent to the simulated town to bring Roxas back to the Organization; however, his first effort was a failure due to Diz's appearance and the restarting of the Twilight Town program. Roxas had no memories of Axel nor any awareness of what was going on. Axel was threatened by Xaldin and Xemnas to be turned into the Dusks, so he tries to recover Roxas without destroying him, keeping in mind the Organization's order to either eliminate Roxas or be destroyed himself. Roxas learns that the two had been best friends from Namine and mentions this to Axel, but his bluff is called when he is unable to remember "their boss's name." Diz then intervenes and Roxas escapes for the Twilight Town mansion. The two meet again at this mansion in the computer room basement. Despite Roxas's recovery of his memories, Axel is hurt from his previous encounter with Roxas and fights him and his dual Keyblades. Axel loses the fight and disappears, choosing not to carry out his mission.
While Sora reawakens with Roxas inside him, Axel is entrusted by Riku to protect Namine. Namine's words, about those who are dear to them despite being Nobodies, strangely moved Axel. During Sora's exploits to the different worlds, Axel appeared before Kairi on a beach across Destiny Islands, intending to kidnap her to draw Sora out. Axel's plan was simple; if Sora were to become a Heartless again, then Roxas would be reborn. However, Kairi escaped through a Corridor of Darkness created by Riku and landed in Twilight Town where she stayed for some time in wait of Sora. Axel, however, followed her to the town and stole her away again, but not long afterward she was taken captive by Saix who was under orders to give Axel something to actually worry about. After the invasion of Radiant Garden by the Heartless, Sora confronted Xemnas, the leader of the Organization. Xemnas decided to take his leave and Axel later greeted Sora. Axel hinted that the Keyblade caused the hearts that composed the Heartless to flee, but refused to say what Organization XIII would do with those hearts. Sora realized that Axel is Kairi's captor, and Axel confirmed this. Though initially seeming unrepentant for his actions, he soon apologized for kidnapping Kairi, and made a hasty exit when Saix appeared.
On the way to The World That Never Was, Sora, Donald, Goofy, and King Mickey are trapped in Betwixt and Between by Nobodies, but Axel arrives to help. Sora and Axel battled the Nobodies, but seeing that the Dusk's numbers were too great, Axel decided to put his entire being and essence into an attack, destroying the Nobodies but sacrificing himself in the process. He did this to save Sora, his best friend's original self, who stayed with him until the moment he faded. He sincerely apologized to Sora for getting Kairi involved. Confused, Sora asked him what he was trying to do and Axel confessed that he wanted to see Roxas, the only one who made him feel like he had a heart. Oddly enough for Axel, Sora made him feel the same way (possibly since Sora and Roxas are one and the same) and used these final words to urge Sora on to rescue Kairi. Axel opened the passageway to the World That Never Was with the last bit of strength he had in him before disappearing into darkness completely. Afterward, Xigbar and Luxord were curious about Axel's foolish and senseless actions; essentially turning against the Organization for the sake of his friendship with Roxas, but Xemnas revealed that Axel's disappearance served to stir Roxas from his rest, claiming Axel's disobedience was not entirely meaningless and pitiful. Xemnas also stated that due to contact with Sora's heart, Axel's own ability to feel emotions could have been affected. Namine, however, backs up this notion in the written novel of the game in which she mentions that Axel never truly died, but rather faded into darkness where he would wander until he would find his heart. Axel made one final appearance to Roxas, right before the latter's mental battle with Sora, where he gives a final farewell to his best friend.