With the climate-controlling Sati still in the hands of the General, the weather within the Matrix took a dramatic turn for the worse, signified by a vivid red hue that caused concern even for the normally aloof Architect. While his Sentinel fleet assaulted the General's base codenamed Stalingrad on the Earth's surface (as seen in the chapter 7.2 cinematic), within the Matrix, Machine forces steadily overthrew the General's systems, even as Zion, with the aid of Seraph, searched for Sati, eventually rescuing the girl from the General's control.
The harried General came to rely more and more on the support of his new ally, the Merovingian. The Merovingian, however, showed a marked disregard for the preservation of the General's commando programs, going so far as to use them as cannon fodder for his own aims, and even secreting some of them within his own hidden constructs, unknown to the General.
Meanwhile, the Merovingian continued his project of eliminating that frequent foil of his plans, the Oracle. He brought a deadly program known as the Apothecary into the Matrix, putting her to work on a code powerful enough to kill the fortune-teller, who managed to complete the killcode despite much interference by the Machines. As a reward for the Apothecary's hard work, the Merovingian, at the instigation of his wife, Persephone, betrayed the Apothecary to the Machines, and she was deleted by a group of hostile operatives.
In the midst of these warring forces, the signal of Morpheus continued to appear to followers of Zion and E Pluribus Neo, declaring that Neo lived, a prisoner of the Machines, and calling on the assembled operatives to fight the Machines in order to rescue the One. Certain inconsistencies and glitches in these signal broadcasts began to raise doubts, however, particularly after E Pluribus Neo found that the signal, made to look like an emergency hovercraft beacon, was in fact originating within the Matrix itself.
The recuperating Cypherite leader, Cryptos, whose Machine overwriting had just been violently purged by Seraph, finally appeared and spoke to some of his operatives, who to their dismay found his mind clouded, and prone to wandering. Evidently, the Machine program that had been controlling him, though overthrown, was now partially merged with his previous, violently anti-Machine psyche.
The Cypherite controller, Veil, viewing her crippled leader with disdain, took command of the organization, leading them in attacks against the Apothecary, and against their mortal foes, E Pluribus Neo. The Cypherites succeeded in capturing an EPN crew, and defended themselves, with help from the Machines, against a counter-attack led by the EPN controller, Shimada. Veil also came to an agreement with the Machines' Agent Pace to resume spying operations in Zion, with the aim of discovering the destination and purpose of large amounts of material and personnel apparently leaving the caves of Zion.
Eventually Cryptos, sufficiently recovered, met with the Machines' Agent Gray, complaining of the pain of his current existence, and asking to be reinserted into the Matrix, as Cypher himself had asked of Agent Smith. Much to the Cypherite's surprise, Agent Gray told him that there was no such procedure.
E Pluribus Neo strove to make further contact with the mysterious Morpheus signals, receiving aid from the Oracle in locating them. The authenticity of the signals came more and more into question as they continued to preach the same message of war against the Machines.
To put these questions to rest, EPN sought to trace the signal to its origin, even in the face of Machine attacks. They succeeded in this endeavor, finding, to the dismay of many, that the signals, encoded in the form of emergency broadcasts from Morpheus' hovercraft, the Nabonidus, were in fact coming from a source within the simulation itself.
EPN also found themselves under increased pressure from the Cypherites, led by the aggressive Veil. They attempted to rescue an EPN crew member captured by the Cypherites, but were unable to reach the operatives, who were guarded by massed forces of Cypherites, Machines, and even some Merovingian operatives.
As the battle for Stalingrad raged in the Real, the Machines began a concerted takeover of the General's systems inside the Matrix, commandeering his helicopter fleet, his communication channels, and even his holographic broadcast.
They closely pursued the Apothecary, taken from their servers and brought into the Matrix by the Merovingian without their consent. The Frenchman meanwhile struck down Agent Pace with a preliminary version of the Apothecary's kill-code destined for the Oracle. The Agent recovered quickly, but seemed altered, adopting a colder, more businesslike demeanor, and demonstrating a heightened enthusiasm for the violent suppression ofSystem enemies.
Following the successful termination of the Apothecary, the Machines located, assaulted, and disabled the General's primary base in the Matrix, found in the complex inhabited by Project Nine soldiers beneath the Abandoned Subway. They then shut down the General's network within the Matrix entirely, and prepared to continue with further operations against the Merovingian, who gave the harried General asylum.
The Merovingian, wanting to kill the Oracle, had the Trainman bring the program known as the Apothecary into the Matrix, and put her to work on a kill-code powerful enough to eliminate the fortune-teller. Blood samples from Sati and from the irradiated ex-Unlimit commander, Beirn, were obtained to increase the code's potency.
The Merovingian wished to test a preliminary version of the code, and the General suggested the Machines' Agent Pace as a test subject. Persephone lured the Agent to a rendezvous where a Merovingian hit squad, armed with kill-code samples, struck down the Agent, much to the Merovingian's delight. Spy reports confirmed that the code had made a lasting impact on the Agent.
The Apothecary eventually completed work on the code, despite continued interference from Machine attacks. Frustrated by the constant threats to her safety, she demanded transport out of the Matrix, which the Merovingian promised to grant her. However, partly at the instigation of Persephone, who had a longstanding feud with the Apothecary, he instead tipped off the Machines as to her location, and the kill-code manufacturer was deleted in an attack by hostile operatives.
Under increasing pressure himself from the Machines for sheltering the General, the Merovingian, unknown to his would-be ally, began smuggling the General's commando programs into hidden constructs under his own control.
Zion worked with Seraph to track down Sati, held prisoner by the General. After fighting through many platoons of the General's commandos, and solving a perplexing assault by Sati doppelgangers created by the General, Sati's program was retrieved and restored to the Oracle, who declared that the girl would soon be well, and able to restore the weather to its normal condition.
Although they succeeded in guarding the Oracle against attacks by the General, Zion decided that her usual home in Mara had become too easy a target for the General and the Merovingian. With Seraph's support, they finally managed to persuade her to leave the neighborhood, and began moving her under guard between secret safehouses across thecity.
Zion also tracked the Morpheus signal, eventually finding it and catching it as a strange glitch occurred, causing it to repeat the same line four times. This raised further suspicions about the signal's true origins. Tracking was complicated by the appearance of die-hard Morpheus supporters, wishing to emulate and further his old agenda.
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Matrix Online: Chapter 7.1: The Search | Matrix Online: Chapter 7.3: Fall of the General |