Like all nanomachine organisms, Cookie wears a leotard like suit that covers most of its torso. In its infant form, its only distinguishing feature is its tuft of light blue hair. Cookie's developed look is seen during Nano's route where she absorbs the DNAs of both Kazuya and Nano, gaining Kazuya's blue eyes and Nano's hairstyle.
Cookie was the only remaining nanomachine organism found inside the abandoned facility on Femto after the Will's short hold of the area. Nano was given full access to the facility's rooms and the team found one signature in the northern most room. The Rune Angel Wing found Cookie inside the room with a console that was different from the rest in the facility. Noa is called over to crack it but she decided that she would like to study it on the Luxiole and has them bring the entire console and Cookie aboard the Luxiole. Nano gives her the name, feeling bad from everyone calling her "it" and "that". Later on, Noa explained Cookie's unique function of absorbing anyone's DNA and replicating it and warned everyone from making direct contact with her. She is kept inside her tank for the majority of the game.In Rico, Anise, and Natsume's routes, Cookie is a non-issue as the three are able to get themselves and Kazuya out of direct contact with Cookie when the glass container shattered. Only in Lily, Kahlua, and Nano's route does Cookie become relevant as they are the ones that make contact with Cookie. In Lily's route, Lily had previously accidentally swatted down Santa Rosa and the residue from her wings led to Cookie's body transforming into a fairy where Lily's consciousness was transferred over from her real body to the new, fairy-sized one. In Kahlua's route, Tequila saves Kazuya from direct contact and Cookie absorbed Tequila's data and grants Tequila her own separate body from Kahlua. Both of these cases are instances of where magic was overly effective on nanomachines.
In Nano's route, Cookie absorbs both Kazuya and Nano's DNA and awakens as a child, inheriting Kazuya's eyes and Nano's hair. Nano is overjoyed at how she has become a mother and treasures Cookie's newfound sentience and adopts her with Kazuya. Cookie showcased her nanomachine ability in being able to fix machinery compared to Nano's ability in healing people. The new "family" relaxed together on Sprite before they were called back to the Luxiole and were assigned to deal with the Luxiole's damaged half and their shuttle receives damage from the debris. Sensing danger to her "parents" Cookie floats off and used her body's own nanomachines to repair the shuttle before it plummeted to a nearby star, saving her "family" but sacrificing her sentience. She would later be recovered in her infant, unaware state.
However, by the end of Nano's route, Cookie is taken out of her stasis and is officially taken as Kazuya and Nano's child, with the latter taking on a more mature appearance.