Matrix Online: Chapter 6.3: Kidnapping
Matrix Online: Chapter 7.2: Desperation
The weather in the simulation took on a distinctly off-color orange hue, as weather patterns suffer to the continued absence of the Oracle's ward, Sati, kidnapped by the ex-Sentinel leader known as "The General." The General struck an alliance with the leader of the Matrix underworld, the Merovingian, bringing the Frenchman into direct conflict with the Machines, who are working to eradicate the General's commando forces.
Zion pursued the Oracle's guardian, Seraph, dramatically returned (as seen in the chapter 7.1 cinematic) after his disappearance while pursuing Sati's kidnappers, and found that he'd been deleting Machine programs from the minds of humans in the Matrix, including the Cypherite leader, Cryptos, who had secretly been under Machine control.
E Pluribus Neo continued their dogged hunt after signals apparently sent by the ex-Zion captain, Morpheus, and finally came across a clear message from the former leader.
As if this, and a certain sanity-shattering party crashed by a notorious Merovingian weren't enough, an outbreak of the Smith Virus threatened to take over the city. Resistance, organized by the Oracle, eventually managed to defeat powerful manifestations of the virus, but as it faded away, it left a message claiming to have taken on a much more insidious, unkillable form.
The Cypherites attempted to understand Seraph's apparent rampage across the city, and to do what they could for his "bluepill" civilian victims. This quest came to an abrupt end when Seraph ambushed the Cypherite leader, Cryptos, performing a strange "exorcism" that left Cryptos extremely disoriented. As his concerned operatives attempted to aid him, Cryptos began uttering strange sounds, which, as his articulation increased, were clearly identified as Machine error codes.
Concluding that Cryptos had been operating under Machine overwriting, removed by Seraph's attack, the Cypherite controller, Veil, ordered Cryptos returned to his ship and put under intensive care, while she assumed interim leadership of the organization.
The Machines were quick to acknowledge that Cryptos had been operating under their guidance, forming the Cypherites as a means of preventing Zion from awakening more than their Truce-allotted 1% of the Matrix' population to the true nature of the simulation. The Machines attempted to renew the terms of their agreement with Veil, but she thus far has put off accepting an accord with the Machines, and relations between the two groups remain uncertain.
EPN put great effort into pinpointing the mysterious signals seen intermittently around the city of late, in which a man resembling the famous Zion war leader, Morpheus, appeared to isolated operatives, delivering messages appearing to allude to the One, Neo, being alive, but held captive by the Machines.
After a difficult process of mining for data concerning a newly detected broadcast of the signal, EPN tracked the signal to the Hypercube monument in Mara, where they were confronted by a clear message from this apparent Morpheus, saying that the Machines had failed, and that Neo was alive, held captive by the Machines, and in need of rescue.
The Machines hacked the General's network in the Matrix, gaining the capability of scanning the exiled program's plans and data. Led by Agent Gray, they captured one of the General's Elite Commandos, gaining enough data on the soldier's stealth routines to enable them to engineer a sensor scan capable of detecting hidden commandos.
Machine pursuit of the General's forces brought them into conflict with the Merovingian, who recently agreed to an alliance with the harassed General. After some frustrating initial engagements, the Machines realized that the Merovingian's opposition may slow down their timetable in eliminating the General.
Meanwhile, the Machines also had to deal with the exposure of their secret control over the Cypherite organization when Seraph found and removed the Machine program that had overwritten Cryptos' mind. Because Seraph's "exorcism" left the Cypherite leader damaged and confused, the Machines attempted to regain control of the Cypherites by striking a deal with Cryptos' second-in-command, Veil, but she remained aloof, showing anger at the long-standing Machine deception.
The Merovingian came to an agreement with the General under which the Merovingian would provide transportation in and out of the Matrix for the General's forces, while the General would help the Merovingian hunt down ingredients necessary for a kill-code capable of terminating the woman who has frustrated so many of his schemes: the Oracle.
The General's commando programs and the Merovingian's operatives worked together to secure a vital ingredient, the last remaining Machine cheat code, held by an unwitting civilian. The General revealed, however, that they would need a special program to put the kill-code together: The Apothecary. Following the General's directions, they tracked down an old code trace of the Apothecary and, from the mouth of an ancient program, learned that the Apothecary was held by the Machines in their mainframes, and could only be retrieved by an old Merovingian employee: the Trainman.
Under growing pressure by the Machines, the Merovingian's operatives located the portal to the Trainman's private construct, hidden in the Abandoned Subway. Leaving an encrypted "note on his doorstep," they eventually coaxed the paranoid Exile out of hiding, and brought him once more into the Merovingian's service.
Zion pursued Seraph, apparently deranged after his plunge from a helicopter into the highly polluted Aqueduct while fighting the commandos who had abducted Sati. They found that although Seraph's attacks on operatives and civilians alike appeared indiscriminate, the victims all shared memory loss after an episode of suspicious personality change in their past.
Zion was eventually able to make contact with Seraph, who revealed that he was nearly done with his work, and that the operatives should be careful to guard their minds. Seraph's removal of the Machine program overwriting the mind of the Cypherite leader, Cryptos, finally made it clear that the Oracle's guardian was, thanks to his exposure to the remains of Machine cheat codes in the Aqueduct, able to detect and remove such programs from the minds of humans.With Zion's assistance, Seraph completed the eradicating of Machine overwriting around the city, and returned to the Oracle's side. The Oracle, however, directed him to rescue Sati from the General, a task that Seraph quickly began, again aided by operatives from Zion.
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