The beginning scenes with Axel and Roxas in Kingdom Hearts II starts off at Twilight Town. The world freezes during the middle of a battle tournament, where dusks appear and fight Roxas. He wins, but is quickly startled by hearing clapping coming from a cloaked man behind him. Roxas doesn't recognize the cloaked figure or his voice. Axel removes his cloak and states, "You really don't remember? It's me. You know, Axel." Roxas still doesn't remember who Axel is or how Axel knows him at all. Axel's chakrams appear in flames, and he tells Roxas that he is coming with him, "conscious or not." Axel initiates a battle, but Roxas is hesitant at first. Finally he accepts, which rightfully excites Axel. Axel is impressed with Roxas' battle techniques once the fight is over. A man named Diz appears and tries to tell Roxas not to believe anything Axel is telling him, and Axel says the same thing back about Diz. Roxas screams for his friends, and the Struggle Competition continues on.

A mysterious man comes and talks to Axel in the White Room. They tell Axel that if Roxas doesn't come back to the Organization soon, he must "pay the price," aka, die. They tell Axel to get rid of him, but Axel gets really uncomfortable about the idea. He tells them that Roxas hasn't turned his back on the Organization yet. The hooded figures seem surprised that Axel is arguing the orders, and reassure him that he is the one who deals with "judgement upon those who disobey the Organization." They then begin to threaten Axel for his own life, striking him a little to the right, slicing his hair a bit in the process. He realizes if he doesn't get Roxas' memories to come back, he will have to kill Roxas so that he doesn't lose his own life.

Roxas ends up at the mansion in Twilight Town to see Namine. He looks at the white walls inside the room where the witch, Namine, is sitting, and he sees a picture of Axel and himself hanging on the wall, both in the Organization cloaks. Roxas stares at it and asks Namine if it was him, and notices that Axel is with him as well. Namine tells him "You ARE best friends..." as if it was a stupid question to wonder why they were together in a photo. Roxas doesn't really believe in what she says, and thinks it's a joke. She asks him if he wants to know who he really is, but Roxas insists that he knows himself better than anyone else, but admits that he doesn't really know whats going on lately. He continues to stare at the drawing of himself and Axel and states, "It's funny... Suddenly I feel like I don't know myself at all... I guess I would like to know. What do you know about me... that I don't?"

Once Roxas leaves the Usual Spot with his friends Hayner, Olette, and Pence, he runs into dusks. After he realizes he is cornered by them, Axel appears. He tells Roxas that he got orders to destroy him if he refuses to come back with him. Roxas looks at Axel and says, "We're... best friends, right?", causing Axel to scratch his head. He tells him that they are, still unsure of the situation. Once he realizes what Roxas said, he excitedly asks Roxas if he truly does remember his life now. Roxas tells him he does in fact remember, but Axel realizes that he has to ask him another question to make sure he really does. He asks him what their boss's name is, but Roxas unfortunately has no response. Axel sighs sadly, and states how he "can't believe this..." The dusks attack Roxas, and Axel is about to fight, when time freezes. Roxas runs away to the sound of Diz's voice. After time unfreezes, Axel sadly says, "The Roxas that I know is long gone. Fine, I see how it is..."

Roxas reenters the White Room and looks at the pictures he saw before. He stops in front of a photo of him in an alleyway of the dark city he saw in his dream before. He gets a huge headache, and then he sees himself cloaked, walking through the dark streets. He passes Axel who is leaning on the wall of a building, crossing his arms. Axel asks him if his mind is truly made up. Roxas stops suddenly and looks at him asking him why the keyblade chose him, telling Axel that he has to know the truth and what is going on with him. Axel screams back that he can't just turn on the organization. The flashback ends, and Roxas' anger rises and walks down to the Basement Hall, where nobodies quickly attack him. After he defeats them all, Axel walks in with his arms crossed. He sarcastically screams "Simply Amazing, Roxas!" Roxas shows that he remembers Axel by stating his name, but Axel refuses to believe him and tells him that he is flattered but he's too late. He makes the room set on fire, and Roxas gets two keyblades in his hands. Axel gets shocked and gets his chakrams. They fight, and Roxas defeats Axel. Roxas stares at Axel and remembers the last time he talked to him before, in the alleyway. During his flashback, Axel tells him that if Roxas gets on their bad side, he will be destroyed. Roxas tells him it wouldn't matter, because nobody would miss him. Axel looked down and says, "that's not true... I would." Roxas snaps out of the flashback as Axel begins to fade away. Axel tells Roxas that he wants to meet him again, in the next life. Roxas promises to be waiting for Axel. Axel laughs and says, "Silly. Just because you have a next life..." as he disappears. Roxas walks over to where Axel vanished and looks down at the ground.

Later on, he tells Sora as he is dying that he "wanted to see Roxas. He...was the only one I liked... He made me I had a heart." Saix comments on how Axel is weak because he fought for something that didn't exist, meaning Roxas and their relationship. Saix noticed that Axel touched Sora's heart, so he believed that "he" awoken too as Saix stares at Roxas's empty Organization seat.

At the Twilight Town clock tower, Roxas is sitting with his head in his lap, and he slowly looks up to hearing a voice ask him if he is finally awakened. Roxas gasps as he sees Axel is standing behind him. Axel tells Roxas that even though Roxas is going to sleep, he wont be able to talk to his consciousness anymore like they are. Roxas sadly realizes he is going back to how he used to be. Axel sits down next to Roxas, as Roxas listens intently to what Axel is about to say. He tells Sora that he's thought a lot about Namine saying Roxas has a heart. He realizes that Namine and himself do not. Roxas tells him he doesn't really know what they all have. Roxas starts to question things about a heart and feelings. Axel doesn't understand, but Roxas just tells him that Sora will find the answer, because Sora is himself. Axel hands Roxas a sea salt ice cream bar. He asks Roxas if he remembers the first day they met and they watched the sunet from the Twilight clock tower. Roxas tells him he remembers and realizes that he has to go. Axel looks extremely sad, as Roxas tells Axel that Sora is waiting for him. Axel looks away and takes a bite out of his ice cream, commenting on how salty it is. They sit in silence, gazing at the view for a few moments. They start to glow. Roxas says, "See you, Axel." as Axel says, "See ya, partner." A single tear falls onto the tower roof.

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