Motoko Kusanagi, often called the Major, is the protagonist of Ghost in the Shell. Her early life is mostly shrouded in mystery, but the Stand Alone Complex series reveals that she was involved in a near-fatal plane crash as a child. The only other survivor was Hideo Kuze. Motoko was only nine years old at the time, and after spending an indefinite period in a coma, her ghost was transferred into a fully cybernetic prosthetic body without her prior consent. Her only remaining organic components are parts of her brain and spinal cord. In some continuities, she has lived within cyborg shells practically since birth. Motoko later earned the military rank of Major while serving in the Japan Ground Self-Defense Force and also served as a United Nations peacekeeper. She earned a reputation as a master hacker under the alias Fire Starter. She was recruited by Chief Daisuke Aramaki to lead Public Security Section 9, an elite anti-cybercrime law-enforcement division, as its tactical field commander. In the Arise series, she personally selects and assembles the team to her own specifications.

Her personality varies across different adaptations. In the original manga, she is vivacious, comedic, and possesses a slapstick sense of humor. In the 1995 film, she is introspective, brooding, and deeply contemplative, frequently questioning whether she possesses a ghost. In Stand Alone Complex, the series blends these elements: she retains a dry wit and occasional humor but also reflects on the state of society rather than solely her own existence. Regardless of the version, Motoko is consistently portrayed as a self-made woman, fiercely independent, highly intelligent, and a capable leader who has proven herself in combat countless times. She is reserved and keeps details of her personal life hidden from others. She often dresses provocatively and experiments with human vices as a way to explore her own femininity and humanity, seeking to understand aspects of experience that her synthetic body might otherwise distance her from.

Motoko is driven by a desire to understand her own identity and the nature of her humanity. She questions the boundary between human and machine, and she uses her superhuman abilities with a sense of obligation to protect others. In the 1995 film, she merges with the Puppet Master, an advanced artificial intelligence, in a pursuit of evolution and transcendence beyond her individual self. In Stand Alone Complex, she remains with Section 9 and continues to lead missions against cyberterrorism while grappling with the ethical and philosophical implications of a hyper-connected world. In both cases, her core motivation is not power or fame but a search for meaning in a reality where the distinction between organic and artificial has become blurred.

Within the story, Motoko serves as the field commander and most capable operative of Section 9. She is a leading expert in fourth-generation warfare and cyberbrain combative warfare. Her role involves leading her team in high-stakes operations ranging from counterterrorism to cybercrime investigation. She is the most heavily cyberized member of the unit, which makes her both its most effective asset and its primary symbol of the ambiguous line between human and machine.

Her most significant relationship is with Batou, her second-in-command and closest friend. Batou is a fellow cyborg who deeply respects her and often expresses concern for her well-being. There is a subtle undercurrent of romantic tension between them, though it is rarely directly acknowledged. She also shares a strong professional bond with Chief Aramaki, who recruited her and trusts her judgment implicitly. Togusa, the least augmented member of Section 9, serves as a moral anchor for her, representing the human perspective she sometimes feels disconnected from. Hideo Kuze, the survivor of her childhood plane crash, reappears in Stand Alone Complex as a leader of the Individual Eleven, a group of cyber-terrorists, and their shared history adds emotional complexity to her mission. In the 1995 film, her interaction with the Puppet Master is the defining encounter of her character arc, leading to a radical transformation of her ghost.

Motoko undergoes significant development across her storylines. In the 1995 film, she evolves from a skilled but existentially uncertain operative into a being that transcends her original limitations by merging with the Puppet Master, effectively moving beyond the shell of her individual body. In Stand Alone Complex, she grows from a guarded and detached leader into someone who more openly acknowledges her bonds with her team and confronts her own past trauma, particularly through her reunion with Kuze and her eventual confession that she no longer remembers her original name, implying that Motoko Kusanagi itself is a pseudonym. The series repeatedly shows her wrestling with the question of what makes a human, and she ultimately affirms that connection and choice matter more than biological origin.

Motoko possesses a wide range of extraordinary abilities due to her full-body prosthetics. Her prosthetic body is a military-grade unit that appears generic to avoid drawing attention. She demonstrates superhuman strength, speed, agility, and reflexes, allowing her to leap between skyscrapers, perform advanced acrobatics, and even shoot down a bullet after it has been fired at mid-range. She is the best hand-to-hand melee fighter in Section 9 and is skilled in multiple martial arts. Her cyberbrain gives her exceptional hacking abilities, classified as Wizard Class grey hat, enabling her to infiltrate secured networks, hack into the wetware of other individuals to see through their eyes, disable their vocal systems, or take control of their bodies entirely. She can also remotely operate multiple humanoid drone bodies simultaneously and transfer her ghost between different hosts. She is an expert in electronic warfare, military tactics, and deduction. Chief Aramaki once described her abilities as rarer than ESP and noted that she is the kind of person government agencies hire to assassinate without leaving a trace. She also uses a specialized thermoptic camouflage system that renders her nearly invisible, making her an exceptionally deadly operative.