Cyborg Ninja

Cyborg Ninja was an alter-ego assumed by several individuals. The name is derived from the high-tech exoskeletons and swords that they utilized, the former of which were developed by Tokugawa Heavy Industries.

Gray Fox
Main article: Gray Fox 

Gray Fox was a former FOXHOUND member in 1995 and Big Boss's most loyal soldier who was supposedly killed during a fist fight in a minefield with Solid Snake in 1999. His body was recovered by Dr. Clark, who fitted him with a prototype exoskeleton in order to use him as a test subject for the Genome Project. The tests also placed him under severe pain, which resulted in him being drugged for several months while experimenting on him, and the aftereffects of the experiment continued to anguish him even after breaking free of the experiments, at least once screaming for medicine. After escaping and killing Dr. Clark in 2003, he would act as the first Cyborg Ninja throughout Liquid Snake's FOXHOUND revolt in 2005. In addition, detailed records for the Cyborg Ninja project were destroyed with the lab when he broke out and escaped. Nastasha Romanenko also heard stories about the project, although she didn't actually think they were true until Snake fought against Gray Fox.

Olga Gurlukovich
Main article: Olga Gurlukovich  Leader of the Gurlukovich Mercenaries Olga Gurlukovich appeared as the second Cyborg Ninja during Solidus Snake's takeover outside Manhattan in 2009. Acting as a double-agent working for both the Sons of Liberty and the Patriots, her role as the Ninja was to assist Raiden and contribute to the recreation of the events that occured in 2005, as scripted by the Patriots. Though she assumed the Cyborg Ninja persona, she never received any cybernetic implants that replaced any part of her body. Although Rosemary claimed that the research notes for the Cyborg Ninja project were lost in the lab's destruction, the fact that the Ninja concept still existed implied that backups of the notes were retrieved to continue the experiments.

Raiden
Main article: Raiden  Raiden was granted a high frequency blade from Olga Gurlukovich in 2009. While undertaking a mission for Big Mama to recover the remains of Big Boss, he was captured and held in Area 51; there, as part of the Patriots' experiments, his head was completely severed from his body from the jaw down. He was fitted with a cyborg body, and left severely wounded to the point of death. He was saved by Dr. Drago Pettrovich Madnar and given artificial white blood. After he was rescued by Big Mama, he used his abilities as the Cyborg Ninja to assist Old Snake during Liquid Ocelot's Insurrection in 2014. Unlike the other Ninjas before him, Raiden made no secret as to his true identity.

Weaponry
All of the Cyborg Ninjas carried a high frequency blade as standard issue. Gray Fox was also outfitted with an arm cannon which fired explosive energy blasts. Raiden holstered a SOCOM pistol as his sidearm. Raiden is said to use the H.F. Blade that Olga gave him, but there are some differences between the swords; Raiden's second blade had a dark grey color, and the handle of the sword was different in that there was no hilt.

Character development
The Cyborg Ninja (サイボーグ忍者) character did not exist in the original concept for Metal Gear Solid and was an original creation by series artist Yoji Shinkawa. Director Hideo Kojima liked the design so much, he decided to incorporate it into the storyline. An unrelated Ninja-type character, Black Ninja, previously appeared in the preceding game, Metal Gear 2: Solid Snake.

In Hideo Kojima's Metal Gear Solid 2 Grand Game Plan, the second Cyborg Ninja was originally intended to have been a machine, before eventually being changed to Olga Gurlukovich in the final game. In one scene, the Ninja would have altered its voice in order to taunt Solid Snake and Otacon, by mimicking Meryl Silverburgh and Sniper Wolf, respectively.

Raiden is the only Cyborg Ninja in the series to survive the events of the game in which he is featured. He is also the only Ninja to have never fought Solid Snake.

Gameplay
After completing Metal Gear Solid twice, Gray Fox's Cyborg exoskeleton swaps its colors so that its red portions become grey and the grey portions become red. Also observable is the color of the "eye" changing from green to red.

Although the Cyborg Ninja has never been playable in any of the main Metal Gear Solid games, he has been featured as a playable character in the expanded versions of the games, along with other game titles:
 * In the racing game Konami Krazy Racers for Game Boy Advance, a Cyborg Ninja resembling Gray Fox, simply called Ninja, is one of the playable racers.
 * In the VR Disc portion of Metal Gear Solid: Integral, the Ninja is playable in three specialized missions, all taking place in the same storehouse. The goals are destroying several straw targets, killing several Genome Soldiers, and assassinating Solid Snake, who's disguised as a Genome Soldier from the neck downward. These same missions are also available in Metal Gear Solid: VR Missions/Special Missions.
 * In Metal Gear Solid 2: Substance, Gray Fox's exoskeleton is an alternate outfit for Raiden's VR missions.
 * Although not a playable character, Gray Fox as the Cyborg Ninja is available as an Assist Trophy in Super Smash Bros Brawl.
 * The SCENE expansion of Metal Gear Online allows the player to play as Cyborg Raiden.
 * In the upcoming game Metal Gear Solid: Rising, Cyborg Raiden is going to be the main playable character.

In Metal Gear Solid 4: Guns of the Patriots, two of Old Snake's FaceCamo faces are Cyborg Raiden (visor open and visor closed). The two can be unlocked by having the Metal Gear Mk. II ram into Naomi Hunter (the adopted sister of Gray Fox) and Sunny (the daughter of Olga Gurlukovich) during mission briefings.