The Nemesis are the villainous force from Metal Black. Metal Black is actually an abbreviated code name for an ambitious anti-Nemesis military project for Military Enforce Totalwar for Absolute Liberty Beam Lesson Aircraft Carrier Kill off.
In the year 2042 a star appeared near the planet Jupiter, propelling asteroids towards Earth. The damage was severe, but soon after started an invasion by an alien race which was named the Nemesis. With little resistance, they successfully take over our planet, intending to plunder our planet of inorganic materials they needed to survive.
Strange molecules started littering the planet, the same ones which were used by the Nemesis weaponry. Scientists study these molecules, calling them "Newalone", thus starting "Project Metal Black" to create a fleet of spacecraft capable of using the same weaponry as the invaders. In addition to Newalon beam, Nemesis possesses ability to have their arsenals merging with Earth's weaponry, converting those infected weapons and use them against Earth's populace. With combination of the converted weapons and their ability to utilize Newalone beam Nemesis' triumph over Earth's militaries was only a matter of time.
To counter Nemesis, A spacecraft was named CF-345 Black Fly which possesses the same ability to utilize Newalone beam. under the project Metal Black. The project was supposed to produce about 20,000 Black Flies and unleash them on the battle against Nemesis. Before the Black Fly had a chance to fly and the Metal Black project can get off the ground however, Earth passes a surrender treat to the aliens, promising to withdraw all of Earth's defense forces, which also applied to Project Metal Black, and never venture out to space ever again. This obviously led to shortage of natural resources and a severe drop on the planet's population.
It was not long before someone discovered about Project Metal Black: John Ford, who was to be a test pilot for CF-345 Black Fly, found the hangar where the Black Fly was stored, deciding to pilot the ship and fight the Nemesis by himself. John suffered tragic loss over his family during Earth-Nemesis War and he was not very pleased with UN's surrender to Nemesis. He manages to defeat the Nemesis forces on Earth, traveling after the Nemesis homeworld, the star which had appeared near Jupiter. It is here John would wage an ultimate showdown with the leader of Nemesis, Omega Zone. While John is waging his last duel against Omega Zone, an illusion that depicts history of mankind and their evolution can be seen on the background one at a time. Depending whether John defeats Omega Zone, players would be treated to two different endings:
If John Ford successfully destroys Omega Zone, immediately and inexplicably all scenes of history of Earth's lifeforms are shown all at once very quickly. Then Earth is shown to be split into two. Then John is shown to be in a fetal position, disappearing into darkness and whole the scene fades out. "WAS ITS PHANTASM THE LAST ATTACKING OR ITS LAST MOMENTS AND WAS THIS FOR REAL OR WAS I DREAMING NOBODY KNOWS YET…" This quote is presumably spoken by John Ford. The final scene of the ending displays a calm ocean under sunset. This ending has confused many players when it came out: did the destruction of Earth really happen, or is it merely an illusion? No one knows...
If John Ford dies either entering final stage but dies before he had a chance to wage a duel against Omega Zone or loses his final duel against Omega Zone and player chooses not to continue, The ending states that The valiant death of John rallies up the rest of surviving Earth's populace and military remnants, they invoke a coup against UN, overthrowing UN and immediately resurrect Project Black Metal. 20,000 Black Flies fly into the homeworld of Nemesis... Shockingly however, the supposed homeworld of Nemesis turns out to be a false information leaked by UN before it is overthrown: not knowing this, 20,000 Black Flies flies off to enemy HQ that does not exist and quite possibly, to their doom. (it should be noted that stage 5's BGMs when Black Fly passes Jupiter and flying towards Nemesis homeworld are named "Doubt" and "Phantasm", subtly hinting that the information regarding Nemesis homeworld is a fake). According to Takatsuna Senba, the producer of Metal Black, says in an interview that Nemesis' homeworld is Mercury, which is in opposite direction of Jupiter.
- Despite the fact that Metal Black is a 2 player co-op game, the story centers around one protagonist John Ford, meaning the game is originally intended to be a single player game.