Metal Gear 2: Solid Snake, released in 1990, takes place in 1999. A similar situation develops to the first game: a rogue nation called Zanzibarland kidnaps Dr. Madnar once more, along with his friend, Doctor Kio Marv, a Czech scientist who has developed a means of creating synthesized crude oil, named OILIX, and thus alleviating the world's energy crisis. Zanzibar Land is led by Big Boss, who un-died somehow, and their new iteration of Metal Gear, the so-called "Metal Gear D". Solid Snake, already retired, is pulled into active duty by the current leader of FOXHOUND, Col. Roy Campbell; he receives radio assistance from a number of characters, including McDonnell "Master" Miller.
Landing in Zanzibarland, Snake comes across Holly White, a CIA operative posing as a freelance journalist, and Gustava Heffner, an agent for the Czech State Security and Dr. Marv's bodyguard, who both assists him in his mission.
Along the way, Snake also makes a disturbing discovery when he is confronted by one of Big Boss' top people, the so-called "Black Ninja". Upon defeating Black Ninja in battle, Snake discovers that his true identity is that of Kyle Schneider, the former leader of the resistance against Outer Heaven. Heavily wounded, Schneider explains that the NATO bombed Outer Heaven indiscriminately after Snake completed his mission, killing and injuring many members of the resistance in the process and devastating the area. When Big Boss showed up again following the bombing campaign, and provided aid to everyone affected by it, Schneider changed his outlook on the man and instead came to support his cause. After a stint in as an operative in NASA's top-secret Extraterrestrial Environment Special Forces Unit, where he was outfitted with an experimental flex armor and reflex-enhancing drugs, Schneider came to Zanzibarland to join Big Boss on more permanent basis. With his last breath, he gives Snake a hint about where to find Dr. Marv, hinting that is what Big Boss wanted.
Instead of finding Dr. Marv at the hinted location though, Snake runs into yet another familiar face, that of Dr. Madnar, who explains that Big Boss had him abducted again, and is now forcing him to work on the Metal Gear D. He is, however, able to provide Snake with Dr. Marv's new location, allowing Snake to finally find the scientist though it turns out that is unable to understand him, as he can only speak Czech and Slovak. Snake joins up with Dr. Madnar, who suggest that they try to seek out the assistance of Gustava to translate for Dr. Marv.
As Snake, Gustava, and Dr. Madnar head toward Zanzibarland's main prison, Gustava is mortally wounded by a missile fired by Metal Gear D, the pilot of which is revealed to be none other than Gray Fox, and Dr. Madnar is recaptured by the enemy. Gustava dies in Snake's arms, but not before giving him the key to the locker where Dr. Marv has hidden the formula for OILIX inside a MSX cartidge.
Snake is able to find Dr. Madnar again, along with the body of Dr. Marv. Dr. Madnar explains that Dr. Marv was tortured for information, and that his heart couldn't take the stress of it. Holly contacts Snake, revealing to him that Dr. Madnar is likely a traitor. Being suspicious of him, she asked the CIA to run a check on his background, finding out that his colleagues in the scientific community in the US had ostracized him for his radical ideas, and that he had voluntarily come to Zanzibarland to oversee the development of the new Metal Gear. With the truth out, Dr. Madnar confesses that angry over being rejected by the US, he deflected to Big Boss' side to seek his revenge, and he admits that he was responsible for the ambush that lead to the death of Gustava as well as accidentally killing Dr. Marv. He then attacks Snake, forcing the soldier to violently incapacitate him.
Snake goes on to confront Gray Fox in the Metal Gear D, and manages to destroy the mech after a fierce battle. Unfortunately, the resulting explosion causes Snake to catch on fire, making him lose most of his gear, while Fox, though injured, is able to steal the OILIX formula from Snake while he was distracted. Snake chases Fox into a minefield, where the renegade challenges him to a fist fight. After an extended fight, Snake emerges victorious, while Fox, exhausted and bleeding out from his wounds, tells Snake about his past, detailing how his life was saved by Big Boss more than once, but in the end that was not the reason why he joined up with him. That decision happened after he felt his shot at a normal life had failed when a romantic relationship turned sour — it turns Gustava was his lover — and he came to believe that could only find his purpose in battle, despite professing a hatred for war itself. Snake offers Fox some reassuring words as he (apparently) expiries, promising him that he will be reunited with Gustava on the other side. Snake then recovers the OILIX formula from his body.
Just then, Snake hears a familiar voice taunting him over the base's PA system. Following the voice into a storage room, Snake once again finds himself face-to-face with the legendary Big Boss. Snake declares that he has come here to Zanzibarland to get rid of the nightmares that he has endured since Outer Heaven. Big Boss tells him, earnestly, that they probably will never go away, before bridging into his Motive Rant, saying that once a soldier has experienced the taste of battle, they will never able to let go of it, and are unable to lead normal lives as they will always hunger for their next battle until they die, revealing that this was his reason for creating Outer Heaven and now Zanzibarland. He wishes to create a world order that is capable of creating perpetual conflicts and wars, so that there will always be new battlefields to send soldiers out to fight and die in. Snake declares that he is still determined to fight and stop him, and Big Boss obliges his wish. Though having lost most of his gear, Snake is still able to improvise a makeshift flamethrower by using his cigarette lighter and a lacquer spray he finds in the storage room. Taking Big Boss by surprise, Snake is able to defeat him, for the second and last time.
Snake is able to meet up with Holly again, and shooting their way out, the two of them manage to make their escape via helicopter. In the aftermath, Campbell offers Snake to rejoin FOXHOUND on a more permanent basis, but Snake rejects this.
