Masaki Aofuji is a fifteen-year-old high school student who serves as the protagonist of FLCL: Shoegaze. Ten years before the story begins, when he was five years old, he witnessed a large cloud of smoke released into the sky from a giant, clothes-iron-shaped building on the outskirts of town. After this event, he began to see glowing, green ghosts everywhere he went, as well as a strange, giant purple bird-like ghost perched atop Tsuganei Tower. No one else can see these apparitions, and this ability makes him unable to fit in with his peers, who distrust him due to his unusual claims.

Masaki has felt like a loner throughout his childhood. His constant visions of ghosts have estranged him from others, and he has resigned himself to being a solitary figure who draws sketches of the ghosts in his notebook. Despite this isolation, his frustration with his situation grows to a breaking point, leading him to plan a drastic course of action. He decides to build a bomb using supplies from his school's chemistry lab, with the goal of infiltrating and destroying the top floor of Tsuganei Tower in the hope of uncovering the truth behind the giant bird only he can see.

His role in the story centers on his partnership with Harumi, an eccentric girl he meets after transferring to Tsuganei High School. Harumi is intrigued by his sketches of ghosts and, upon discovering his bomb-making plan, decides to help him. Together, they trespass into the tower, and their actions draw the attention of the police and the Bureau of Interstellar Immigration, including Chief Kanda and the adult Kana Koumoto. Masaki's troubled emotions and his N.O. channel, the same psychic energy that has driven FLCL's supernatural events, become a focal point of the story. His uncontrolled N.O. reaction inside his head lights the bomb's fuse, and events quickly escalate beyond his control.

Personality-wise, Masaki is introverted, withdrawn, and initially passive, but he possesses a deep well of frustration and a desire for change. He becomes easily flustered around Harumi, yet he sees her as a kindred spirit. Throughout the series, he develops from a resigned loner into someone willing to act on his feelings and take responsibility for the consequences of his abilities. A key relationship is his bond with Harumi, which evolves from a tentative partnership into a romantic connection. He also interacts with Kana Koumoto, who tries to guide or stop him, and is manipulated by Kanda, who attempts to sow distrust between him and Harumi to provoke a greater N.O. reaction.

Notable abilities include his unique perception of ghosts, which are manifestations of another dimension, and his possession of a strong N.O. channel. His N.O. channel allows him to affect reality, manifesting the ghosts visibly to everyone during a critical moment and eventually causing a giant flying snake-like creature, identified as Atomsk, to emerge from his forehead and absorb the tower's power source. At the story's conclusion, Masaki develops the ability to cross over into an alternate universe, allowing him to visit the original male version of Harumi on a Mars colony, demonstrating that his power has grown far beyond his initial need to merely see ghosts. He remains able to see the green ghosts even after the dimensional split is resolved, though they are once again invisible to everyone else.