2125 A.D.
A period of relative peace follows the various Maverick uprisings. A reploid miliary called the Repliforce is established during this period; Zero is assigned, for a time, to act as liason between the Maverick Hunters and Repliforce. During her assignment she befriends a Colonel Aiken, whose sister Iris immediately takes a shine to Zero. Zero and Iris become romantically involved when Iris is later assigned to Maverick Hunter Headquarters as a navigator; while Zero has feelings for X, she fears how he'd react if something happened to her again.2126 A.D.
Repliforce is framed for an attack on the floating city Sky Lagoon. In the aftermath, Repliforce is ordered to stand down operations and submit to investigations. The General of Repliforce declares independence for his army and sets out to create a reploid nation in space. X and Zero are assigned to track down key Repliforce officers and detain them, but find they've all gone maverick one by one. Iris attempts to defuse the situation as a representative of Repliforce, but tensions are too high on both sides.
The Hunters discover that one of their own had been subverted by Sigma, and was in fact behind the Sky Lagoon crash. This information comes too late, as Repliforce has already constructed a space station--which X and Zero deduce Sigma is going to use as a weapon. The pair attempt to get to the station undetected, but a double-agent within the Maverick Hunters tips Sigma off. X is drawn into a conflict with Colonel Aiken, while Zero is confronted by Iris. X defeats Aiken; Zero accidentally destroys Iris while trying to disable her. Enraged, she goes on to confront Sigma while X attempts to settle things with the General of Repliforce. Sigma seems to have taken newfound interest in Zero's past, but she powers through his attempts to manipulate her; once Sigma is defeated, X and Zero deploy the station's self-destruct at the General's request. Survivors of Repliforce are brought into custody, and any remaining equipment is seized. Though the war is brought to a conclusive end, X and Zero are both left with mental scars by the incident.
2128 A.D.
A Dr. Kivane Locke is hired by Dr. Cain as a systems engineer and robotics technician. She upgrades the Maverick Hunter HQ with a hybrid reploid mainframe system--a reploid AI in control of a central computer with the processing power of a major server farm. Lucia, as the system is called, quickly settles into her role of coordinating Maverick Hunter operations. Dr. Cain oversees the construction of a new commander for Unit 14, a reploid named Kieran, who is initiated and trained at the European Maverick Hunter facility before being transferred to North America. Protoman, using the name Blues, joins the Maverick Hunters to keep an eye on X and Zero. A maverick robot calling itself Xenos begins making trouble for the Hunters, who are unable to determine his origins.
2129 A.D.
Two unidentified entities are encountered during an attack by Xenos. They drive the maverick off before giving the Hunters the slip, but one of them bears a strong resemblance to Xenos and is presumed by the Hunters to be the maverick's creator. All Hunter units receive standing orders to bring the two into custody if they're encountered again.
2131 A.D.
Sigma makes a return, staging an attack on New York City--but it is discovered to be a ploy, as the destruction of his body causes the Sigma Virus to begin spreading en masse. At the same time, a mercenary hired by Sigma captures the long-defunct Eurasia colony and sets it on a collision course with Earth. The Maverick Hunters scramble to devise a means of stopping it. With all other options exhausted and only hours left before impact, Zero volunteers to crash a space shuttle into the colony. It is successfully destroyed and Zero's escape pod is recovered, but irradiated fragments of the colony still cause significant damage to the surface as they fall from orbit.
Zero immediately sets out on her own to find and destroy Sigma, leaving the other Hunters to attempt tracing her coordinates. X finally arrives on the scene to find both Zero and Sigma critically damaged. He unwisely turns his back on Sigma to tend to Zero, resulting in both of them receiving a laser blast through the chest. X shuts down immediately, but Zero uses 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. While responding to a maverick attack, X encounters what appears to be a ghost of Zero, who briefly assists him before teleporting away. Multiple sightings of this 'ghost' are reported in a short time, accompanied by a new virus that appears to be inducing some sort of waking nightmare in every reploid it infects. A reploid named Isoc makes a public announcement on the subject, calling it the Zero Nightmare.
X takes exception to Zero's name being dragged through the mud, and takes it upon himself to track down Isoc's investigators and find out what they know. Those he is able to find attack him without warning. Tracking a third, X is confronted by the Zero 'ghost,' who pleads with him to abandon the Hunters and join her in spreading the Nightmare Virus. X wastes no time and dispatches Nightmare Zero, only for the real Zero to reveal herself shortly afterward. She returns to Hunter HQ with X, claiming it doesn't matter how she was brought back--though the reality is she has no idea.
The Hunters learn Isoc's investigators were all constructed by the same man, a reploid named Gate with a very checkered past. They track down three of the investigators, but discover the rest have already been destroyed. Continued sightings of Zero by other Hunter teams leave her and X baffled. With all of Isoc's team dispatched however, the Maverick Hunters receive a communication from Gate explaining that he's the one behind the Zero Nightmare, and challenging Zero to prove herself to him. She rises to the challenge, and though Gate proves himself a fearsome opponent--augmented with Zero's RDNA data--she triumphs. Gate attempts to pull a trump card in defeat, activating a half-rebuilt Sigma. He overpowers Gate and retreats. Zero returns to Hunter HQ, leaving immediately with X once Lucia has managed to track Sigma's location. En route, the pair find Zero's second doppelganger in a heap--a blue-armored, male reploid. Zero keeps an eye on him while X continues on to deal with Sigma.
2134 A.D.
Ikari, the second Zero doppelganger constructed by Gate, joins the Maverick Hunters. Zero and X become romantically involved. Tranfer of personnel around the various Maverick Hunter bases, in the aftermath of the Eurasia incident, has left the main headquarters in New York somewhat understaffed. Xenos makes a single-handed attack against the base that kills many of the newer recruits and destroys nearly all of X's equipment.
Current events in The Other Side proceed from this point.