When Amiko's mother was killed during a giant dragon's rampage through Tokyo, her mother made Wolverine promise to take care of her daughter with her dying breath. Since the dragon had arrived in Tokyo from the fabricated planet Battleworld, and had somehow grown to its monstrous size, Wolverine felt partly responsible, and accepted his burden of honor.
As a full-time X-Man, Wolverine was unable to care for Amiko personally, but he did foster her with his fianceé Mariko Yashida. Amiko lived with Mariko for a few years, enjoying the plush life that the head of Clan Yashida was able to provide. She saw Logan on rare occasions.
Amiko also got to meet Kitty Pryde. Shadowcat was brainwashed by Ogun when she came to Japan. After Kitty broke her conditioning, she hid Amiko and Mariko from Ogun, who had come to kill them. Yukio was then able to get Amiko and her mother to a safehouse. Following Ogun's defeat, Amiko went for ice cream with Kitty, Logan and Mariko.
When Mariko was assassinated by the Hand, however, no legal plans existed to care for Amiko, and she was placed in the Japanese foster care system. Logan assumed all was well, but the truth was that Amiko was living with abusive people. Furthermore, she clung to the memory of her savior "samurai Logan," which distanced herself from her peers. 
Eventually, Logan discovered that the money he had been sending his daughter was being stolen by her foster parents and he came to investigate the situation. Logan got Amiko out, gave the foster parents a what for, and asked Yukio to take over guardianship, with financial support from the Silver Samurai, now the head of Clan Yashida. In return, Logan gave back the Yashida Honor Sword.
A few months later, Amiko was captured by a filmmaker named Akatora. When Logan went to visit Amiko, he was attacked by the Hand, employed by Akatora, who was also using torture to brainwash Amiko into killing Logan. She was eventually freed by Wolverine and Shirohana, another mutant, though at the time it seemed that the brainwashing was still in effect.
However, no evidence of Akatora's influence was evident months later, when Logan visited her in Tokyo. Amiko had been learning martial arts from Yukio, and had gotten into some fights. Just as Logan and Yukio arrived at a tea joint where Amiko and her friends hung out, Amiko punched a guy through the store window. Though Yukio was upset, Amiko defended her actions as helping out her friend who was being harassed by the now-unconscious cad. Amiko ran off, and Logan tracked her and tried to reconcile with her. Later that night, though, Amiko and Yukio were kidnapped by Gom Kaishek, to be used as leverage over Wolverine, whom Gom hoped would kill his brother, Lord Haan.
After being transported to Gom's hideout, Amiko managed to loosen her bonds, allowing her and Yukio to escape, just as Wolverine arrived. Amiko met up with Wolverine, but demanded to help him find Yukio, who then had gone after Kia, Gom's sister. Wolverine reluctantly agreed to allow Amiko to accompany him, but left her to care for the wounded Silver Samurai, whose interactions with Clan Kaishek had precipitated the entire affair.
Amiko, however, ended up disobeying orders and snuck into the Kaishek fortress, arriving to attack Kia at a critical juncture. Unfortunately, her fighting skills were insufficient, and Kia caught her and threatened to use her as a hostage. Wolverine arrived in the nick of time, freeing Amiko and then telling her to get Yukio out while he disposed of Kia.
Months later, Amiko went to a carnival with Logan, who tried to win a teddy bear for her, but his uncanny accuracy with a knife caused the crowd to freak when they realized he was a mutant, so he gave Amiko some money and left.
Owing to her lineage, she has the potential to develop mystical abilities.
Amiko has limited training in the martial arts.
- Amiko's name was originally Akiko. Her name was changed to Amiko by accident, and the change stuck.
- 38 Appearances of Amiko Kobayashi (Earth-616)
- Media Amiko Kobayashi (Earth-616) was Mentioned in
- 5 Images featuring Amiko Kobayashi (Earth-616)
- 2 Quotations by or about Amiko Kobayashi (Earth-616)
- Character Gallery: Amiko Kobayashi (Earth-616)
- Amiko Kobayashi (Earth-616) at Wikipedia.org
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