Niobe holds a private meeting on a building rooftop, telling her followers that things will get tough in fighting the Frenchman because they need more firepower. The General’s helicopter flies overhead, commandos drop down on the meeting, and fighting breaks out since Niobe believes they are under attack. The General stops the fighting and proposes a deal to unite in fighting the Merovingian, which Niobe agrees to.
Cypherites increase their attacks on Zion recruitment teams in order to stop any more bluepills from being awakened “against their will”. Zion operatives raid a masked network station and find a report that the Union Hill Cryptos box has encountered an error and that they must increase security at that box, again strengthening the connections between Cryptos and Cypherites. Masked men indeed begin spawning around the Union Hill area.
Zion decides to further investigate Cryptos, who used to be a Zion captain before Neo established the truce. Cryptos’s crew has since “retired” to lives in the Matrix, and operatives are sent to hack a bluepill database to find out where the crew lives. The hack is successful and reveals that only two of the crew are still alive. The first crewmember has since married a bluepill and left the real world behind her, very unhappy to find Zion knocking at her door. She says she stayed away from Cryptos, Morpheus and other “saviors”, which raises the question of whether or not Cryptos was anything like Morpheus. The second interview reveals that Cryptos was a strong protester against Machine civilization but also good friends with Cypher of the Nebuchadnezzar.
Zion tries to dig further into Cryptos’s history, but all Zion archive files show signs of tampering. Zion finally links two of their current operatives who recently went missing while investigating Cypherite activity. Zion begins tracking down these two soldiers, eventually linking them to a friend of theirs who is a “wild card” known to indulge in the Matrix’s simulations and lies. These suspicions are confirmed as they overcome heavy Cypherite activity at the suspect’s address and finally rescue the first soldier locked up in the basement for “knowing too much”. The first soldier overheard the guards talking about the other location, so the team is able to catch the Cypherites off guard and rescue the other soldier.
The rescued soldiers recall that just after the truce, Cryptos suddenly became even more fanatically anti-Machine and believed the Matrix is evil. He stopped talking to people and wanted to destroy the Matrix, even urging people to wake sleepers even if they weren’t ready. This conflicts with recent information about Cryptos: apparently he went from a fanatic redpill to an equally fanatic Cypherite.
Zion eventually traces the tampered Cryptos files back to an address within the Matrix. Operatives are sent to obtain the original files, and it turns out the site is a popular redpill party spot, an ideal cover for a Cypherite base. Operatives are denied access to the site’s computer systems by Zion guards, despite obvious clearance. Tyndall isn’t surprised as she suspected an inside job, and she gives operatives clearance to detain the rebellious guards. After doing so, they coax a partier into accessing the system and find no Zion archive files, but the data is uploaded for analysis, which reveals the computer system was merely a router for the actual archive hack. Teams are sent to other locations, but all prove equally void of archive files. Tyndall suspects their activities are being tracked and countered.
At a dead end, Zion sends an undercover operative to a suspected gathering of illegal traders of hacked information. All sorts of hacked information, access codes and even blue pills are for sale. After striking a deal with one of the traders, the operative is sent to a contact who apparently deals in “this sort of thing”. At the given location, Zion operatives meet heavy rogue resistance, including the contact they were sent to find. After dealing with the rebels, they find the missing archive files on the active computer, learning that Cryptos jacked into the Matrix without permission a couple of weeks into the truce, encountered some agent activity, then completely disappeared off his operator’s screen. He returned an hour later and refused to talk about where he had been. Soon, Cryptos was missing from both the Matrix and the real, only recently returning as a completely changed man.
Zion learns about the meeting between Veil and the Merovingian, and using their newfound allegiance, they have the General dispatch elite commandos to assist in further operations.
After interviewing some of Cryptos’s old bluepill contacts, Zion learns that he used to perform in one of the city’s many warehouse clubs. Anome instantly assumes this must be Cryptos’s secret base and sends not only a squad of Zion operatives to storm the place but also calls in Commando support. The arrogant Anome is surprised that Cryptos is nowhere to be found, but the warehouse is crawling with exiles. The exile leader says she bought the warehouse from its former redpill owner, Acuben, fair and square and that they have no right to attack. After obtaining Acuben’s contact card, the team leaves the exiles to deal with the mess. Anome appears confused, and he is convinced the exiles must have been working for the Merovingian who in turn must be working for Cryptos, and he believes Acuben will turn out to be Cryptos in disguise.
At Acuben’s address, the squad is met with heavy masked resistance. They fight through to the Cypherite redpill and question her. She protests that Cryptos has preached nothing but peace and harmony between machine and human since his re-arrival in the Matrix. Then, in mid-sentence, she falls to the ground, dead, her cranial jack apparently tampered in the real world, probably by a Cypherite. Searching her body finds an audio file, a conversation between Cryptos and a kidnapped soldier, which has Cryptos saying that the only way to defeat the Machines is to commit mass genocide and deprive Machines of their power. He justifies this by saying sleepers are hardly alive as it’s just a “TV show beamed to their heads”.
Just as the Zion operatives are about to leave, the operator picks up a heavily encrypted signal being transmitted into the building, and an on-site phone begins to ring. One of the team picks it up and is greeted by the calm, calculated voice of Veil. She says she had to cut the conversation with Acuben short because “loose lips sink hovercrafts”, but that she hopes they can talk more again… personally sometime soon. Anome doesn’t believe the operatives and think they are making it up to hide their “failure”.
Since Veil’s release, Cypherites have increased in numbers, efficiency and discipline. Zion sends an operative to interview an ex-Cypherite who recently returned to the cause of Zion. He says that Veil transformed Cypherites from simple masked bandits holding guns into sophisticated operatives with strict procedures and secret facilities. He gives the address of one of the training centers but warns it’s probably gone since Cypherites move often. As expected, no Cypherites are found, but they find an old simulacrum program of Veil herself, introducing herself as the Cypherite mission controller and beginning a training program. Before any valuable information can be obtained, the simulacrum is remotely shut down by an external signal, but what little data they got was saved onto a hard disk.
Zion traces the signal that shut the Veil program down back to its base of operations, which they go clear. Another training program is uncovered, this time of Cryptos. He says he is the leader of the Cypherites, who are dedicated to letting people live the best possible lives. The program continues in subsequent rooms as 3 Cryptos simulacrums glorify and give praise to the masked cause, which Tyndall clearly identifies as propaganda.
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