Naminé first appears in Chain of Memories, being held hostage by Organization XIII. Under orders from the Organization, she alters Sora's memories to remember her as a close friend from Destiny Islands. When Axel releases Naminé under his own agenda, she reveals herself and the truth to Sora. When Marluxia is defeated, Naminé puts Sora, Donald, and Goofy to sleep for a year in order to restore the chains of memories which she broke. Naminé also saves Riku in "Reverse/Rebirth" from Zexion by teaching him not to fear the darkness. When they meet in person, she offers to lock away the darkness of his heart at the cost of his memories, but he refuses the offer, opting to battle the darkness himself. Afterwards, she contacts DiZ to help protect Sora, Donald, and Goofy until they awaken. However, Xemnas's creation of the Replica Xion from Sora's memories, and Xion's later death and return to Sora, hampers her ability to restore Sora's memory, forcing DiZ to have Riku obtain Roxas for her to complete her task.
In Kingdom Hearts II, Naminé is revealed to be a "special Nobody" born from Kairi's heart when it left Sora's body. As Kairi had no darkness in her heart, her heart hid within Sora's body instead of becoming a Heartless when Destiny Islands was consumed by darkness. When Sora impaled himself with the dark Keyblade, his body and soul were used to create not only Roxas, but Naminé as well. As a result of this, she has none of Kairi's memories. Naminé's special birth in conjunction with the fact that Kairi's heart had been in direct contact with Sora's is why Naminé's special powers could only affect the memories of Sora and those whose hearts are connected to his. Despite DiZ's orders, Naminé visits Roxas in the virtual Twilight Town to help him discover his true identity. DiZ instructs Riku to destroy Naminé since she is no longer useful. However, a new scene in Kingdom Hearts II Final Mix reveals that Riku lets her go with Axel in return for her help in Castle Oblivion. After meeting with Roxas once more through Sora after Xemnas' apparent defeat, she fuses with Kairi to complete her.
She later cameos in the mobile game Kingdom Hearts coded where a data copy of her uses Jiminy's Journal to contact Mickey and reveal to him the fate of Terra's group. She also briefly appears in Kingdom Hearts: Birth by Sleep, shown drawing a picture of Sora sitting alone on a Paopu tree in his Kingdom Hearts II attire on Destiny Islands and says Sora's name. If Namine possessed a heart, she could be in love with Roxas, as Kairi is in love with Sora.