Uncomfortable with how unpredictable the actions of Cypherites have become, Zion sends operatives on missions to track and observe Cypherite groups in hopes of learning more.
A Zion spy team traces Cypherites back to
Zion pursues a lead on Cryptos, a man who says Cryptos’s boxes were stolen from his warehouse. The man says Cryptos had been using his warehouse for storage, and one day the boxes were suddenly gone. The owner still has Cryptos’s deposit, a watch, which Zionists take to help with the investigation. The watch is traced back to a jewelry store run by an exile named The Jeweler. While waiting to see the exile, operatives talk to bluepill workers who say they saw Cryptos talking to men in suits and ties with earpieces (agents, of course) the day Cryptos bought the watch. The Jeweler confirms the watch to be his work and that Cryptos requested that the watch not run. The Jeweler gives the team Cryptos’s customer file, including home address.
Anome, who is in charge of the investigation, orders that Cryptos’s watch be personally uploaded to him so he can wear it next time he goes “slumming”. Operatives are then sent to the address of Cryptos’s home and are met with Neo/Trinity look-alikes, mostly teenagers (clearly E Pluribus Neo members), who attack the team, believing them to be Cypherites. The attackers are put down, and searching the house reveals nothing useful. Anome declares the mission a failure and doesn’t believe the team’s story about the attackers, saying the team is just making excuses.
Zion determines that Neo/Trinity look-alikes confront Cypherites and end up interfering with Zion investigations. Also, several hovercrafts have cut contact with Zion, and Zion is unable to research the crew because their data has been wiped from the mainframe. Commander Lock suspect “Neoites” who have gone renegade. Using a backup copy of the missing ships crew data, Tyndall tracks their location in the Matrix, and a Zion team is sent in to question the renegade redpills. The operatives are attacked by the youth who again mistake them for Cypherites, and all of the rebels are killed. Searching one of the dead bodies reveals written operating orders, a clear sign of the group’s disorganization. Tyndall hopes to return the rebels to the Zion cause while their chain of command is apparently weak.
The operatives go to the address on the acquired operating orders and find another renegade hideout. After fighting through more rebellious youths, they gain access to a computer and see an open conversation window with Fracastoro, who talks about how the Cypherites are “going down” and Shimada knowing what she’s doing. Tyndall recognizes this name and begins running checks. Operatives are sent to the original of the conversation window to question Fracastoro. Arriving at the traced renegade base, operatives are again met with attack, but the mention of Shimada’s name instantly stops the fighting, and the rebels lead the Zion team to their leader, Fracastoro, who orders 2 of his men to escort the Zion team to Shimada so she can decide for herself whether or not to trust them.
Tyndall reports to the team being escorted and says that Shimada is a Zionite and in fact a captain of one of the missing ships. Shimada tells them that their group, E Pluribus Neo, is devoted to following the teachings and ideals set out by Neo himself, believing that every human should be allowed the chance of freedom. She requests the team leave quietly. Tyndall feels that Shimada is young, naïve and hiding something but still believes the group can be dealt with peacefully. However, if the group isn’t dealt with swiftly, EPN’s awakenings could cause the Machines' power supply to become threatened, and Zion could be accused of breaking the truce.
Brian, a member of E Pluribus Neo, has second thoughts about joining the group and contacts Zion. Anome is put in charge and sends an operative to talk to Brian. Brian confesses to still being a follower of EPN’s ideals but feels the leadership is far too weak - not Shimada’s leadership but The Kid’s. Anome calls The Kid a “no good punk” and says they should take him out “execution style” - Anome seems to have something personal against him.
Anome says he knows where one of The Kid’s friends hangs out in the Matrix and sends operatives to question the redpill. They stumble upon a small meeting of EPN followers. The team is spotted and immediately attacked. After the rebels are put down, Anome formulates a plan to contact another one of The Kid’s associates and say the first group sent them with urgent news for the Kid’s ears only just before they were attacked, in hopes that the foolish youth would lead them straight to The Kid. The plan works, but upon arrival at the Kid’s location, a jamming signal is activated, and the operatives are lead into a room full of E Pluribus Neo crusaders. They apparently knew of Anome’s plot all along. The Kid, who calls himself Michael (see Animatrix: Kid's Story), explains that EPN is neither lacking organization nor dedication, and the large numbers are growing every day because they are recruiting from all organizations, not just Zion, since the organization consists of all who agree with Neo’s beliefs. The team pulls out and Anome becomes furious, promising that all those traitors will burn for thinking they’re better than Zion.
The Zion council decides to leave E Pluribus Neo alone for the time being because of their connections to the human race’s savior, also saying that attacking them would be suicide because of Morpheus rumors on the rise again. Zion refocuses on their campaign against the Merovingian.
Zion sends operatives to an exile communications base in order to plant a bug in the mainframe. However, doing so is deemed impossible due to how heavily it is guarded, so Zion uses commando forces to create a disturbance in another area, leaving the mainframe vulnerable. The mission is a success despite fears that the Merovingian forces might already be using the new EMP style device. Zion’s top commanding officers begin planning an all out offensive against the Merovingian’s remaining troops, to be set into motion in the next few days or few months.
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