Makoto Shido serves as a primary protagonist with brown eyes and black hair. She typically wears a black tank top under a purple denim jacket, a purple skirt, and pink rubber shoes. Her prized possession is the Idaten Bike Neptune, a specialized mountain bike gifted by her older brother, Kyoichi Shido, who taught her mountain biking. Neptune later reveals water-riding capabilities. Makoto demonstrates kindness, helpfulness, and sensitivity, though prone to mood swings and occasional temper outbursts, after which she attempts to rectify the situation. Her effectiveness significantly increases when operating with strong determination. She maintains a close friendship with her elementary school classmates, Sho Yamato and Kakeru Sakamaki. Her relationship with Sho involves childhood connections and occasional quarrels when angered, though she often takes care of him. Makoto holds profound admiration for Kyoichi, viewing him as a role model and aspiring to emulate him. She fiercely defends him against accusations of villainy and deeply cares about his well-being. She enjoys sweet foods like chocolate sundaes and junk food.

Her story begins when she, alongside Sho and Kakeru, is transported to the X-Zone during a mountain bike challenge against Gabu Samejima. Within this realm, thorough cleaning during her first race inside a cave reveals Neptune's golden emblem, confirming its identity as a legendary Idaten Bike. While navigating the X-Zone, Makoto assumes responsibilities like maintaining the group’s truck, preparing meals, and performing cleaning duties. Her journey involves significant character development concerning Kyoichi. Initially unaware of his presence in the X-Zone, she eventually encounters him while he conceals his identity to protect her. She experiences vivid hallucinations of her family, including memories of her brother's past kindness. When confronting Arthur about Kyoichi, she insists on knowing the truth despite attempts to shield her, asserting her capability to handle danger. A pivotal moment occurs during a snowstorm when Kyoichi saves her from a cliff fall at personal risk. Later, she intervenes diplomatically to prevent infighting among the Four Kings and Gabu, emphasizing unity against their common adversary, Team X.

Her resilience becomes evident when Kyoichi, under a dark emblem's influence, imprisons her in a cellar alongside Gabu. During confinement, they share chocolate, and she discovers Kyoichi's hidden message on a glass window, revealing his plan to escape the emblem's control. After freeing themselves, she locates the Idaten Bikes and relays Kyoichi's strategy to the others. She actively participates in his rescue during a race, pulling a disconnected cable on a steep hill just in time to prevent his defeat. Makoto extends her role into competitive racing, collecting emblems alongside teammates to facilitate their return home. She engages in a duel race partnering with Sho; during one critical moment when Sho's Flame Kaiser sustains damage, she battles opponents using Neptune, unleashing its powers to protect Sho's platinum emblem. Her technical mountain biking skills develop throughout the series, balancing biking with other activities differently than characters solely focused on competition. Her interactions with Gabu Samejima evolve from initial dislike to reluctant cooperation, particularly during shared captivity and collaboration to foil Kyoichi's possessed state, developing a working dynamic despite Gabu's abrasive personality.