
2125 A.D.
The period of relative peace following the various Maverick uprisings is more than welcome for everybody. By this point a reploid army, called the Repliforce, has been established. Zero is assigned, for a time, to act as liason between the Maverick Hunters and the Repliforce; during her assignment, she befriends a Colonel Aiken, whose sister Iris immediately takes a shine to Zero. Zero begins dating Iris after a time, though she has deep feelings for X that she won't admit to out of fear of hurting him if something would happen to her again.2126 A.D.
Things have been quiet for too long, at least from the point of view of Sigma, who has been hiding in the shadows for the last seven years. He sets events into motion by hiring the leader of Maverick Hunter Unit 14--Magma Dragoon--to crash Sky Lagoon, a floating city constructed in 2110, into the ground. In exchange, Dragoon gets the opportunity to fight Zero, something he's wanted to do since joining the Maverick Hunters. Sigma then disguises a giant Maverick with Repliforce insignias and sets it loose on Sky Lagoon. Zero and X are sent to deal with the situation, but upon their arrival Dragoon has already disabled the city's engines, blaming it on the 'Repliforce' Maverick. The three of them teleport out just before the city crashes into the ground, killing thousands of people and injuring thousands more. Zero returns to deal with the Maverick (stopping to help Iris to safety along the way, as she had been in the city), only to be confronted by Colonel Aiken afterward. He thanks Zero for saving Iris, but Zero is forced to ask him if Repliforce really had anything to do with the attack. Aiken, insulted, refuses to return to Hunter Base with her and teleports out.
Repliforce quickly begins a coup, claiming independence and setting out to create a reploid nation in space. Meanwhile, Sigma is infecting key Repliforce officers with the Maverick Virus, causing the Hunters to have to take action against them, which only serves to further anger the Repliforce. Iris shows up at Hunter Base before too long, attempting to dissuade Zero from taking any further action out of fear that she or Aiken will be destroyed. Zero can't, however, simply let the Maverick Repliforce members roam free; she and X cut a swath through them, eventually coming across the traitor Dragoon and dispatching him after learning what really happened at Sky Lagoon and getting cryptic advice from him regarding Sigma.
Meanwhile, Repliforce has finished constructing a space station in Earth orbit, but the officers Sigma is controlling have been converting its power systems into a weapon capable of destroying the entire planet. X and Zero eventually piece together what's going on and head up there, splitting up en route to the station's bridge; X is confronted by a Hunter recruit named Double, who--go figure--turns out to be a double-agent working for Sigma, while Zero is forced to fight Iris, who's decided she can't let the conflict go any further. X dispatches Double and quickly gets drawn into a fight with Colonel Aiken, while Zero tries to reason with Iris, to no avail. Just as X defeats Aiken, Zero miscalculates a disabling shot and detonates the power core of Iris' ride armor, effectively ending her lover's life. In the time she spends mourning Iris' death, X goes on to confront Repliforce's General, but just as their fight comes to a crescendo, Sigma wrests control of the station from Repliforce and aims the weapon at Earth. The General pleads with X to stop Sigma before he can destroy Earth, but Zero's already beaten him there; she confronts Sigma with a viciousness she hasn't posessed since her discovery at Skull Fortress, utterly destroying every weapon he can throw at her. She eventually reduces him to scrap and she and X set the station to self-destruct, fleeing in an escape pod. At this point Zero breaks down and pours her heart out to X, who comforts her as best he can.
2128 A.D.
There has been another period of uneasy peace following Sigma's last uprising, in which a number of things has happened. First and foremost, the Maverick Hunters have a number of new recruits; Kivane Locke, a cyborg of enigmatic origin, whom Dr. Cain has hired for her expertise in robotics; Blues, who has decided to join in order to keep an eye on his younger siblings; and Kieran, a new reploid constructed by Dr. Cain for--much like Sigma--the sole purpose of being a Maverick Hunter. Secondly, a mysterious Maverick calling himself Xenos has appeared on the scene, stirring up a fairly good-sized amount of trouble before fading into the shadows, only to reappear at completely random times and start all over. The Hunters are baffled as to his origins and motives; his design seems to pre-date even X, and he has no known affiliation with Sigma or any previously-empowered Maverick organizations.
2129 A.D.
On top of the threat of Xenos, the Hunters have also encountered two other mysterious beings named Are-X and Walker. The two don't seem to be a direct threat, but their sporadic appearances began almost immediately after Xenos' arrival on the scene and that in itself is suspect as far as the Hunters are concerned. In addition to this, Walker's similarity in appearance to both Xenos AND Kieran is far too remarkable to be considered coincidental. Walker and Are-X have done nothing but act cryptic around the Hunters thus far, but they are still regarded as possible hostiles and extreme caution is advised to all Hunters who encounter them.
2131 A.D.
A Maverick attack on New York City is quickly discovered to be the work of a revived Sigma; X and Zero are dispatched to intercept him before he can cause anymore damage. Upon stopping him, however, they discover that his defeat was planned, and that through his battle body's spectacular explosion, the Sigma Virus is quickly spreading across the planet--as well as the fact that a virus-riddled space station called Eurasia is on a direct collision course with Earth. With the Sigma Virus spreading world-wide through the atmosphere, reploids all over the planet are turning Maverick, leaving the Hunters severely crippled. Assessment of the situation leads them to the conclusion that they have two options--attempt to destroy the station with an antique laser cannon called the Enigma, or crash a space shuttle into it, in hopes the impact will break it up enough that the collision won't cause as much damage to Earth.
With only sixteen hours before impact, they frantically set out to repair the Enigma and the shuttle, gathering the parts they need from any source they can find--understandably, they're forced to take the parts forcefully from a number of Mavericks that might have otherwise cooperated. The Enigma's attack fails, and Zero takes it upon herself to pilot the shuttle into the station. The plan ultimately succeeds; Zero manages to launch the shuttle's emergency pod and escapes the explosion with relatively minor damage. However, the explosion is close enough to Earth to do considerable damage to the surface of the planet; irradiated chunks of the station rain down for hours, devistating anything in their path.
With Sigma still on the loose however, the debris storm from Eurasia is considered the least of their worries. Zero immediately sets out on her own to finish him, leaving the other Hunters to attempt to trace her coordinates. X finally arrives at the battle scene to find both of them heavilly damaged. He unwisely turns his back on Sigma to tend to Zero, resulting in the both of them receiving a laser blast through the chest. X shuts down immediately, but Zero manages to use the last of her power to deliver a killing blow to Sigma. A recovery team arrives shortly after, but only X is found; there's no trace of Zero, aside from her saber.
Several weeks pass; X is repaired in that time and clean-up efforts have begun. However, progress is soon hindered by strange occurances involving what is reportedly a ghost of Zero--who has been pronounced dead. X is having a rather haunting dream of Zero when the reports start to come in; he's awakened to respond to a Maverick attack at the crash site of Sky Lagoon. When he arrives, the Maverick in question isn't registering on Hunter Base's sensors, but that doesn't in any way prevent it from attacking him. A counterattack is rendered impossible when X sees a purple-armored Zero teleport in, dispatch the Maverick with one swing of her black Z-Saber, and teleport out without saying a word. Alia sees it over the sensors as well, and suggests X return to base. Before he can, he's attacked by a reploid calling himself High Max. Though X is unable to inflict any damage on him, High Max retreats shortly into the fight. Alia and X discover shortly thereafter that their bizarre sighting coincides with reports from across the globe; also accompanying the phantom Zero's appearances though is some sort of new virus that seems to put infected reploids in a nightmare-like state, causing them to attack their fellow workers at random. Several days pass before a public announcement is made by a reploid named Isoc, in which he explains that a team of investigators--led by none other than High Max--is looking into the phenomena, which he refers to as the Zero Nightmare.
X is infuriated by Isoc's accusations toward Zero, and pleads his case with Hunter commander Signas. Signas agrees to let X track down Isoc's investigators and question them as to what they know, assigning Alia to work with him exclusively for the mission. The first two investigators he finds--Metal Shark Player and Ground Scarab--attack him without warning, and he's forced to destroy both of them.
In the lair of the defeated Scarab, X is confronted by the 'ghost' of Zero. At this point he's already not entirely convinced she's the real thing, and her actions soon prove him correct--she pleads with him to leave the Hunters and join her in her endeavor to spread chaos and fear through the Nightmare Virus. X nobly refuses her request and dispatches her, using the real Zero's saber to finish the job in a touch of poetic justice. Before he returns to the Hunter Base however, he's confronted by another--none other, in fact, than the real Zero. After a heartfelt reunion (during which Zero rather vaguely tells X that it doesn't matter how she was resurrected, nor does she care), the two return to Hunter Base together, only to find out that the two investigators that attacked X were classified as Mavericks several years prior.
What little information they manage to gather on the rest of the investigators reveals no connection between any of them, except that several of them were created by a reploid scientist named Gate--a former colleague and close friend of Alia's, who in recent years has made a rather sordid reputation for himself by dabbling in subjects of questionable morality, as well as performing a good deal of barely-legal research. X and Zero spend the following week or so tracking down three of the remaining investigators--Blaze Phoenix, Infinity Mijinion, and Blizzard Wolf, but upon searching for the final three--Rain Turtle, Shield Sheldon, and
Skye Yammark, the two Hunters find out that they've already been destroyed. Other Hunters in the immediate area of all three locations claim that they spotted who they thought was Zero before the investigators were destroyed, leaving her and X totally baffled.
They return to Hunter Base, no closer to solving the mystery of the Nightmare phenomena than when they started--until they receive a communique from Gate, explaining that he's the one behind it all, in hopes of rooting out the weakest of the reploids and creating a utopia for those that remain. He challenges Zero to prove herself to him--if she can find his lab--before cutting the connection. Alia manages to track his transmission to one of the Eurasia impact sites, and Zero wastes no time taking Gate up on his challenge. She stops briefly on the way in to destroy High Max--who turns out to be one of Gate's creations--before confronting Gate himself. He proves to be quite a challenging opponent, but Zero manages to defeat him regardless. In desperation, he does the unthinkable and activates his trump card. Gate is well aware of the risks of this course of action, but proceeds with it anyway; unfortunately, in his damaged state he's no match for even a half-completed Sigma.
Zero gives chase to the resurrected ex-Hunter, but he manages to slip away from her. She returns to base and desperately attempts to track him down, grabbing X and teleporting to his location as soon as she gets a set of coordinates. When they arrive, they find something unexpected--a blue-armored, inexplicably male doppleganger of Zero lays damaged and deactivated in their path. As Zero is pretty beat up from her fight with Gate as it is, X pleads with her to stay behind and keep an eye on the duplicate. She reluctantly stays, letting X take care of the malfunctioning Sigma.
2134 A.D.
Three years later, Zero's doppleganger--IKARI Zero--has become a valued addition to the Maverick Hunters. Zero has finally confessed her feelings to X by this point and the two of them are happily dating. A large enough percentage of the damage to Earth's atmosphere has been repaired that humans can start fully populating the surface again, and Dr. Cain has established several more Maverick Hunter bases around the world. Tranfer of personnel has left the main headquarters in New York somewhat understaffed, however. Xenos continues to make himself a threat; he makes a single-handed attack against the base that kills many of the newer recruits and destroys virtually all of the armor that Dr. Light has given X over the years. Things all come to a crescendo, however, when...
...Well, why don't we just all see what happens?