This is the version I'm going with...
Cypherites
• [12.2.1] Cryptos informs the Cypherites that they will form a line between the Oligarchs and the bluepills of the Matrix, to act as protectors. A battle ensues between the Cypherites and tons of Override Programs. Tesarova appears, toys with the group, and then brutally kills Cryptos.
• [12.2.1] Veil takes over as the leader of the Cypherites, stating that "This is how it should have been to begin with."
• [13.1.1] Veil sends operatives to make contact with an old member of the Cypherites, who went into hiding in the real, some time ago. After a great deal of effort, eventually players make contact with Gemaskeerd, an old friend of Veil's, who is invited back into the fray to attend a meeting with Veil and several others.
• [13.1.1] Cypherite operatives learn that after Enmascarado's death, Gemaskeerd went into the real, to wait for things to blow over. When Cryptos took control of the Cypherites, Gemaskeerd had considered returning... but he didn't agree with the ‘passive' stance that Cryptos took with the organization. Veil says that she agrees, and that now things will be run "their way, and to Hell with everyone else."
E Pluribus Neo
• [12.2.1] EPN offers Ghost and Trinity refuge, while they hide from the Oligarchs and the Machines. There is an interesting interaction between Ghost, Trinity, and the Kid. In the end, Kid orders EPN to prepare for large-scale detonations of CPD's, to eliminate any chance of Ghost and Trinity being tracked by the Machines or the Oligarchs.
• [12.2.1] Trinity expresses a mixture of astonishment and worry concerning what Kid has become.
• [12.2.3] Dislodge is appointed the position of Controller, in place of the recently deceased Shimada.
• [12.3.3] Trinity encounters the Morpheus Simulacrum. The two share an interesting dialogue concerning her, Neo, purpose, and the real Morpheus. Trinity explains that she doesn't want to live this way, and that she'd rather be dead than be trapped in the Matrix once more.
• [13.1.1] E Pluribus Neo learns of Neo's fate. Kid is overwhelmed with anger, and prepares to send EPN to its doom, if it's necessary, to get revenge. Before he can get too fired up, however, they find themselves under attack from the Cypherites.
Machines
• [12.2.1] The Architect expresses that a reset of the simulation is imminent. All operatives are to continue to humor the Oligarchs, while bluepills are put to sleep in preparation of the reset. Agents will be dispatched to begin purging the simulation of all redpills not aligned with the system.
• [12.2.1] Agent Gray expresses to Machine operatives that there is a theoretical solution to the problems concerning the Oligarchs, and that it is currently being tested, before a decision can be made as to whether implementation should be attempted.
• [12.2.1] Intensifying their search for the Biological Interface Program, Helian and Tesarova initiate the "Eyes in the Sky" throughout the simulation. Meanwhile, the system begins changing billboards and signs throughout the Matrix to send messages to non-machine aligned redpills. "Jack Out Now. Discomfort Will Be Extreme."
• [12.2.1] Squads of Agents begin appearing at random, to begin dispatching redpills from the simulation.
• [12.3.2] The origins of the Oligarchs are revealed to Machinist operatives, along with the true status of Neo's body.
• [12.3.3] The Machines implement their last resort against the Oligarchs, and begin a contained infection Tesarova with a pure copy of the Smith Virus, overwriting her completely, and beginning an catastrophic effect inside the Oligarch Network. All Overrides and Oligarchs are overwritten by the Smith Virus. Because the Oligarchs function through a series of codes derived from Neo, the Smith Infection results in their destruction. Sentinels descend upon the Oligarchs in the Real, destroying their advanced fighters. Neo's body is found, within the Oligarch City, and has been in stasis since it was obtained by them, shortly after his death. The Machines return the body to Machine City, where it will remain in stasis.
Merovingians
• [12.2.1] The Merovingian receives intelligence that the Machines are preparing to reboot the simulation, and begins to make preparations for the survival of his empire.
• [12.2.1] Merovingian operatives are sent to speak with various members of the Merovingian's organization, and partnering organizations, about the impending situation. Beirn is unaccounted for, and it is up to the operatives to make sure he receives notification from the organization.
• [12.2.2] Merovingian operatives meet with the Effectuator, who is in the process of making necessary calculations for transport between the Matrix and the Merovingian's Survival Construct.
• [12.3.3] The Merovingian, Persephone, Flood, Ookami, Malphas, The Effectuator, Beirn, The Twins leave for their own personal survival construct, telling the Merovingian operatives that they're "on their own."
• [12.3.3] As all of the Merovingian's loyals prepare to be transported to the survival construct, everyone is caught by surprise when Persephone and The Effectuator betray the Merovingian. The Merovingian is sent to Blackwood instead, while Persephone takes control of the organization.
• [13.1.1] Persephone returns with her new loyal subjects, and makes contact with the operatives through Flood. She explains that her betrayal of her husband has been something that she has planned for some time now; she was simply waiting for the next system reboot to occur, which looked like it would never happen.
• [13.1.2] Flood is outraged by Persephone's actions, and begins an underground effort to free the Merovingian from Blackwood, unbeknownst to Persephone and the others.
• [13.1.3] Flood's attempts are discovered, and Flood is targeted by Persephone and her followers, forcing him to go on the run. Flood seeks out the operatives, calling them "old friends," to help him restore rightful order.
Zion
• [12.2.1] Niobe takes a personal interest in the Ghost/Trinity situation, and jacks in, in an attempt to aid both them and EPN.
• [12.3.1] Zion orders for all operatives to be recalled from the Matrix, in preparation of the system reset. All operatives begin spreading the word, similar to the way Niobe and Ghost did in Enter The Matrix, when they called the meeting regarding the information obtained by the Hovercraft Osiris.
• [12.3.1] Machines and Oligarchs begin coming down hard on Zion, tracing every telephone call that is made, in an attempt to force Trinity to the surface.
• [13.1.1] Zion is contacted by Seraph, and operatives are sent to meet with him. Seraph leads Zion Operatives through the White Hallways, and directly to the Oracle, who turns out to be alive after all.