Goemon Ishikawa XIII is introduced as a formidable adversary to Arsène Lupin III. In the original manga, Goemon first appears as a very dangerous enemy, seeking to kill Lupin after the master thief infiltrated his clan to steal a secret alchemical formula. His cover was blown by Fujiko Mine, who was Goemon's girlfriend at the time. Goemon makes several attempts on Lupin's life, ranging from hiring assassins, such as Daisuke Jigen, to planting bombs in Lupin's belongings. However, he eventually decides he could learn more by working with Lupin rather than against him, abruptly switching his allegiance. His place in the group is cemented when Lupin ruins a court case against the man who murdered Goemon's uncle, allowing Goemon to take his revenge publicly and brutally. In the first anime series, his recruitment follows a similar path, where both he and Lupin outwit a common enemy, leading Goemon to slice Lupin's car in half and then join the gang after a moment of understanding.

Personality wise, Goemon is the archetypical stoic and brave warrior. He is typically quiet, mellow, and aloof, but he can occasionally explode with frustration, admire beautiful women, or even scream in fright, which are usually treated as humorous moments. He holds an extreme sense of pride in his abilities and feels deep shame and remorse when he fails at a task or succumbs to a weakness, often leaving to meditate or train to rid himself of these flaws. His most frequent pastime is meditation, during which he is often so deeply focused that he cannot be moved, even when threatened. Goemon shows strong allegiance to Japanese culture; he dresses in a traditional hakama, prefers his hair long and unevenly cut, exclusively eats Japanese cuisine, and is a firm believer in Buddhism and Shinto. His drink of choice is sake, and he enjoys activities like fishing, attending noh theater, and listening to enka music. A notable weakness for Goemon is women; he tends to trust those who seem innocent, which often lands him in trouble, while he also fears that sultry women will distract him from his training and tends to flee or blush in immodest situations.

Goemon's primary motivation is the mastery of his skills and the adherence to his personal code of honor. He participates in Lupin's exploits less frequently than Jigen and only on a when-interested basis. He is easily annoyed by Lupin's antics, especially his infatuation with women, and will occasionally oppose Lupin directly when a job conflicts with his morals. He has even promised that his last act with Lupin will be to deliver his deathblow. Despite this, he does not hesitate to help Lupin in serious situations, especially when Lupin works for a just cause, demonstrating a deep, underlying loyalty.

Within the Lupin gang, Goemon has distinct relationships with each member. His bond with Lupin starts as a professional one but develops into true loyalty over time. He has a much more amicable relationship with Jigen, seeing him as a fellow honorable warrior and a trustworthy partner, and the two are frequently paired together on jobs. In contrast, his relationship with Fujiko Mine is strained. Although she was once his girlfriend in the manga, he grows to distrust her due to her exploitative nature. On occasion, he will still ally himself with her if their goals align and she makes no attempt to betray him.

As the thirteenth generation descendant of the legendary renegade samurai Ishikawa Goemon, his character naturally develops through his journeys and internal struggles. He constantly hones his martial arts skills and often confronts challenges that test his pride and principles. Breaking his sword, the Zantetsuken, is a recurring source of shame that leads him to periods of intense training and self-reflection. His development is often shown through his evolving relationships, such as the broken engagement with Murasaki Suminawa of the Suminawa clan, when he decides he is unworthy of being her husband.

Goemon's most notable ability is his mastery of several classic Japanese martial arts, including Kenjutsu, Battōjutsu, Jujutsu, Aikido, and Karate. This training grants him extraordinary physical prowess, including near-superhuman speed, underwater breath control, and the ability to easily defeat multiple armed attackers with his bare hands. His trademark asset is his sword, the Zantetsuken, known in the original manga as the Ryusei. The Zantetsuken is a legendary blade capable of cutting through virtually any substance, including flying bullets, steel girders, automobiles, and even multi-storied buildings. Despite this deadly power, Goemon prefers to incapacitate rather than kill, usually destroying his opponents' weapons and clothing. After performing such a non-lethal cut, he is known for his catchphrase, which laments that he has cut another worthless object. He also possesses other skills common to the Lupin gang, such as driving, piloting, and speaking multiple languages.