The Neo Black Ghost is the successor of the original Black Ghost terrorist organization, striving to follow in their footsteps for world domination and war.
At present, there are two distinct incarnations of the organization that exist throughout the different continuities in the series. One is the Neo Black Ghost seen in the Weekly Shonen Sunday run of the manga, and the other appears through episodes 22 to 50 of the 1979 series. While bearing the same name, both have considerable differences, with the manga version of the organization having a sporadic role.
Neo Black Ghost was initially considered to appear in Cyborg 009 The Movie: Legend of the Super Galaxy in earliest planning (due to their presence in the manga at the time), but the idea did not pan out.
- President/"Skull": A leader bearing somewhat of a similarity to the original Skull with his costume when he initially appears. He debuts in the Golden Triangle arc art the start of the run, and while he is unnamed in the actual story, the Ishinomori Character Guide identifies him by "Skull" due to the resemblance. He re-appears in the "Aphrodite" arc.
- Julia Manoda: A colleague of Dr. Gilmore, from his days at the original Black Ghost organization. She appears in "The Arctic Ghost". Within the arc, it is explained that she had fallen in love with Dr. Gilmore after he surgically repaired her face, but was against the idea of him betraying Black Ghost. The two fell out due to this, and Julia remained loyal to Black Ghost after his and the 00 cyborgs' rebellion. She would resurface in the 1980s, being revealed to be one of the heads of Neo Black Ghost and having a base at the North Pole.
- Aphrodite: A boss of Neo Black Ghost that appears in the "Aphrodite" (Empire of Pleasure and Beauty) arc. She met the head of the Neo Black Ghost organization ten years prior to the arc, and developed Aphrodite Island as their base.
- "Kyoko": An esper working under the Neo Black Ghost that appears in the "Eyes and Ears" one-shot. She telepathically manipulates a young man named Yuuji under the guise of being the ghost of his deceased girlfriend Kyoko, and orders him to kill 003. Yuuji eventually meets up with the false Kyoko and learns that the Neo Black Ghost plan to use him for his powers, instead opting to kill both himself and this young woman by leaping off the cliff.
- Pharaoh Virus scientist: Appears in the "Pharaoh Virus" story. He attempts to steal the mummified corpse of Tutankhamen and spread a biological virus through Egypt, and extort money from the people to sell them the cure. He is visibly modeled after Dr. Tenma, from Tetsuwan Atom/Astro Boy.
A group of generic Neo Black Ghost soldiers are also seen at the start of the chapter "Computopia", being defeated by the 00 Cyborg Team. Uniformed soldiers bearing some resemblance to the Cyborg Men are shown in both "Golden Triangle" and "Arctic Ghost".
- Shiva, Brahma, and Vishnu: Three cybernetic triplet brothers leading the organization.
- Dr. Gamo Whisky: The father of 001. After the defeat of the original Black Ghost, he was responsible for having remodeled the triplets.
- Kilados: A subordinate of Dr. Whisky's, seen in the final arc of the 1979 series.
- Gorg: A minor notable villain seen as part of the organization's intelligence bureau in episode 33. He leads the trio calling themselves The Messengers from Hell and was responsible for converting his adoptive son into a cyborg.
- Tsutomu: The adoptive son of Gorg, and based off of Cyborg 0013 of the manga. He has an Accelerator much like 009, and can mentally control a giant robot.