When Roxas was first created, Xemnas found him in front of the old mansion in Twilight Town. When
asked to join Organization XIII, he refused, and was left to wander (the real) Twilight Town. It
was then that, Roxas first saw Hayner, Pence, and Olette. Despite knowing that he couldn't feel, he
was jealous. Seeing the look on Roxas' face bothered Axel, who was watching from a distance, and he
confronted him. After a moment of talking, Axel convinced Roxas to join the Organization XIII.
In Kingdom Hearts: 358/2 Days, Xemnas places Roxas under Axel's tutelage after he joins the Organization. The two bond quickly, eating sea-salt ice cream together at the Twilight Town Train Station after their various missions. As their friendship grows, Axel began to demonstrate emotions and feelings due to his time with Roxas, Sora's Heart. Axel and Roxas are present when Xion joins the Organization, but are not able to spend much time with her yet (her gender is unknown at this point) as Axel is sent to Castle Oblivion by Sa�x to deal with the traitors.
While these events are not shown in Kingdom Hearts: 358/2 Days, they are included in Chain
of Memories, while Sora and Riku are wandering around Castle Oblivion. Axel is working for both
parties of the already divided Organization XIII - Marluxia and, of course, Sa�x. Marluxia, teamed
up with Larxene, seek to use Sora's powers to take over Xemnas and the rest of the Organization
through Namin�, who will alter Sora's memories. The others are partnered with Sa�x, who realize
Marluxia's ambitions and try to counteract by using Riku to destroy Sora. Axel battles Sora to test
him and is defeated. Being the first Organization member to reveal his face, he gladly gives up a
card as Sora's reward so he will progress further into the castle. In his conversation with Larxene,
he shows an interest in the fact that Sora was able to maintain his self-consciousness even after
becoming a Heartless.
After Vexen nearly reveals the existence of Roxas to Sora, Axel is ordered by Marluxia to dispose of Vexen. Axel does so effortlessly and is accepted by Marluxia and Larxene into their conspiracy. Using this to his advantage, he allows Namin� to escape and contact Sora. Later on, Axel confronts Marluxia, allowing him to figure out the fact that Axel is actually working as a double agent. Referencing his previous order to rid the Organization of traitors, Axel is about to attack Marluxia even at the cost of Namin�'s life but is interrupted by Sora, whom he fights instead. At the end of the battle, Axel pretends to have fallen and says "I don't deserve this after I helped you..." before he vanishes.
After completing his mission to exterminate the "traitors", Axel returns to the
World That Never Was. While he was away, Roxas has been spending time with Xion, doing what he and
Axel would. It's obvious that he feels replaced and becomes jealous; pushing Xion away. Soon enough,
at the suggestions of Roxas, the two being to spend time as a trio, and Axel warms up to her.
Some time later, Axel finds himself before Sa�x, the second-in-command, and reveals that he regrets not being able to talk with Sa�x as he could with Roxas and Xion. Sa�x reminds Axel of the friendship they shared before becoming Nobodies, and the plans they had to take over the Organization. Sa�x also indirectly belittles Axel for having a friendship with the two lowest ranking Nobody's.
Later, after Xion discovers who and what she really is, she decides she wants to leave the Organization.
She ends up battling with Axel in front of the Old Mansion of Twilight Town, with Axel claiming he would
do "whatever it took to bring her back". This shows his true feelings for her; he did the same thing
later on for Roxas when he was leaving. He viewed her as a friend now, and did not want to lose that.
Though Xion escapes, Axel chases her throughout the town and eventually catches up to her in front of
Roxas... he manages to knock Xion unconscious during their battle and bring her back to the Castle That
Never Was, but Xion later escapes again and attacks Roxas in a crazed state.
Ultimately, she is absorbed by Roxas and ceases to exist, as she was an imperfect replica of Sora; made from his leaked memories. Before she is gone, she convinces Roxas to leave the Organization and learn about his true self, which he does. Axel catches up to him before his departure and pleads for him to stay, as he did with Xion, but Roxas leaves anyway. Feeling distraught and betrayed yet again, he returns to his quarters where he discovers a popsicle stick which reads "WINNER", a gift left by Roxas, which he had been saving for Axel all along.
When Roxas leave the Organization, he is plagued with questions as to why he has a Keyblade and
subconsciously seeks out Sora. His demeanor changes, which is obvious during his last conversations with
Axel. Soon after, Roxas is captured by Riku and put in DiZ's Digital Twilight Town. Here, he has no memory
of his time spent in the Organization with Xion and Axel; his memory has wiped clean 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 failed due to DiZ's appearance and the restarting of the Twilight Town program. Roxas was dumbfounded by Axel's appearance, lacking any memories of him and awareness of what was going on. Pressed by the threats by Xaldin and Xemnas, Axel tries yet again to recover Roxas without killing him, keeping in mind the Organization's order to either eliminate Roxas or be eliminated.
Upon meeting Namin�, Roxas learns that he and Axel had been best friends. He mentions this to Axel, who
is hopeful at first that his best friend was coming to, but his hopes are dashed when Roxas is unable
to remember the name of their boss. DiZ then intervenes again and Roxas escapes for the Twilight Town
mansion. The two meet again at this mansion in the computer room basement. Despite Roxas's slow 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 sadly disappears, choosing not to carry out this mission on his former best friend.
While Sora reawakens with Roxas inside him, Axel is entrusted by Riku to protect Namin�.
During Sora's journey to the different worlds, Axel appears before Kairi, intending to kidnap her to
lure in Sora. Axel realizes that if he could transform Sora into a Heartless, Roxas would be born yet again...
therefore, bringing back his best friend. Kairi is hesitant of Axel, then escapes through a corridor of
darkness created by Riku, landing her in Twilight Town to stay there for some time in wait of Sora. However,
Axel comes for her once more, but not long afterwards she is taken captive by Sa�x instead under orders to give
Axel something to "actually worry about".
After the massive invasion of Radiant Garden by the Heartless, Sora confronts Xemnas, the leader of
Organization XIII. After a short conversation, Xemnas decides to take his leave, and Axel is there to greet a
confused Sora. Axel hints/explains that this mysterious Keyblade causes the hearts that composed the Heartless
to flee and that this is useful to the Organization, however, he refuses to say what they plan to do with
those hearts. Axel also apologizes for losing Kairi, but flees for his life and body before Sa�x appears, for
the Organization threatened to turn him into a Dusk if he failed to bring back Roxas, which he didn't do.
Axel does not appear again until Sora, Donald, Goofy, and King Mickey are trapped in Betwixt and Between by Dusks on their way to the World That Never Was. Suddenly, Axel arrives to help and they begin to battle the ever-growing number of Dusks. Axel realizes that the number of enemies are too great for the two of them and decides to put every ounce of his energy into one massive attack to destroy the Nobodies in one blow and to save Sora, who stayed with him until the moment he faded away. During his final moments, he sincerely apologized to Sora for getting Kairi involved in this situation. Confused, Sora asked him what he was trying to do and Axel confessed that all he wanted was to see Roxas; the only one who made him feel like he had a heart. He also confesses that, oddly enough, Sora made him feel the same way.
Before his death, Axel used his final words to urge Sora on to rescue Kairi and opens the passageway to the
World That Never Was with the last bit of strength he had before disappearing into darkness completely. Afterward,
Xigbar and Luxord were curious about Axel doing something as foolish as 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 not entirely meaningless and pitiful.
This is when Xemnas states that due to his close contact with Sora's heart, which was Roxas, Axel's own ability to feel emotions began to evolve. Namin� backs up this notion in the written manga 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 in Roxas's flashback where he gives a final farewell to his best friend.