Kyle Schneider

Kyle Schneider, better known by the war alias The Black Ninja, was formerly the leader of Outer Heaven resistance movement before becoming a Zanzibar Land mercenary in Metal Gear 2: Solid Snake, sent to kill the titular protagonist.

Backstory
Schneider was originally an architect forced by Outer Heaven to design their barracks. Drawing the line when his wife and child died, Schneider formed and led a resistance group against the PMC and used his military genius to plan the resistance's next movements.

Metal Gear
When the FOXHOUND rookie operative known as Solid Snake was assigned to rescue a captured peer imprisoned by Outer Heaven, Schneider provided the agent with intelligence about the internal structure of the base, as he was the head of its construction. Kyle was originally presumed deceased after Snake lost his frequency, as the resistance leader was just about to reveal the true identity of Outer Heaven's president, who was later found out to be Snake's commanding officer.

Metal Gear 2: Solid Snake
However, Snake's assumption of Kyle's death was later revealed to be incorrect in 1999, where the former was called back in the field to intercept Zanzibar Land. After the fall of Outer Heaven, Kyle was kidnapped by NATO and used in NASA experiments to make him a super-soldier, injecting him with strength-granting drugs and forcefully toughening him up to be the ultimate ninja. This granted him his codename Black Ninja. However, Black Ninja's unit was disbanded, having him retreat and join Big Boss' Zanzibar Land PMC where he became a skilled assassin. Black Ninja forgave Big Boss, who was the one behind the former's imprisonment as an architect, as the Zanzibar Land president took pity on him and his men and granted them food and shelter.

After being assigned to assassinate Solid Snake and disguising himself as a doctor (Kio Marv) Snake was sent to rescue, Black Ninja confronted his former ally, but was defeated despite his enhanced physical condition. Moments from dying thanks to his mortal wounds, the Black Ninja revealed to Snake his identity, where the real Marv was, and that Big Boss was the sole man behind Zanzibar Land's formation, knowing that telling Snake this was what Big Boss would've wanted.

Trivia

 * Kyle shares a striking resemblance to Gray Fox, another anti-villain in the Metal Gear series. Both were originally war operatives and allies to Solid Snake, were forced to become physically peaked ninjas and fought Snake before dying yet redeeming themselves.