Niobe reminds Zion of its partnership with the General and reveals that the commando soldiers are inexperienced when fighting other exile programs. She has agreed to help train the Generalís commandos and requests that all operatives willing to help with training do so. Many in the ranks of Zion are troubled by this since trust and respect for the General is low. To address these concerns, Niobe holds a meeting at the Jacobs Ladder club [inside]. She begins by informing the operatives of her decision to divert Zion liaison status to her new crew aboard the Logos II in case she is not available within the Matrix. She assures everyone that she distrusts the General just as much as he does them, and that the agreement does not imply trust. She also reminds everyone that the alliance with the General is the only way Zion stands a chance against the Merovingian in avenging Morpheusís death. The meeting ends badly as operatives are shouting at Niobe in protest. She leaves her new crewmate Seraneth to clear the area and get the operatives to understand.
A team of commandos is assigned to accompany Zionists in an upcoming mission against the Merovingian. Anome warns the operatives not to look bad in front of their allies. They successfully clear out one of the local exile hideouts. Pleased with the progress, the General sends out one of his elite commandos to assist and study the operations in future assignments. They proceed to clear out another tougher exile hideout, Anome seeming almost desperate to show the commandos what Zion is capable of. The General congratulates the operatives and says that the extensive data gathered by the elite commando is being converted into superior anti-exile subroutines as they speak.
Tyndall notices that some of the Effectuatorís dire lupines have been unusually active and sees this as the perfect opportunity to test the effectiveness of the Generalís commandos. The Zionites and commandos are successful, and the upgraded commandos seem to be effective. The General holds a meeting and says that it may be possible to create special weapons for use against certain exile defenses, and he needs operatives to lead a group of specially programmed commandos to further test the theory and collect the data they need. Tyndall agrees to help, and they are successful in their first mission, fighting a tough battle against many dire lupines.
The Generalís liaison informs Tyndall that the anti-exile weaponry is almost complete and that another mission is necessary to collect data on one more exile type. The mission is a success, and the General orders his coders to begin work on the new weapon. The Zion Council orders that operatives help guard the Generalís coder labs in case of attack since this new weapon is so vital. Several of the labs are sieged by exile forces, but Zion and commando guard teams fight them off.
The Generalís coders finish their work on the anti-exile weapon, and mass distribution to Zion operatives begins. The weapons are enhanced versions of wooden stakes, silver bullets and holy water, dealing significantly more damage to exiles than their regular versions.
The Zion Council decides to temporarily join forces with Machines in order to better combat the Merovingianís forces. The General shows distrust for Machine civilization but respects the wishes of the council. Anome is put in charge of giving Machines the anti-exile weaponry. One Zion operative makes his way to the trade location, and sensors indicate an alarming number of exiles in the area, indicating the Merovingian was tipped off to the location of the meeting. With the help of squads to deal with the exiles, the commando meets the agent and the deal is a success, but not before having to fight off many waves of attackers. Under new procedures, the Zion operative is required to debrief by a senior member in case of ďcontaminationĒ, and Ghost himself does the debriefing, assuring the operative of the necessity to work with Machines even though nobody trusts them.
Tyndall announces that itís time to launch an offensive against the Merovingian now that the anti-exile weaponry is in their arsenal. A recon squad is sent to a Merovingian redpill base to gather intelligence about other Merovingian bases. While the Merovingian redpills are quickly killed and waiting to reconstruct, the team finds one redpill who regrets joining the Merovingian after only one day of service to him. He promises the team the information theyíre after if they take him back into the ranks of Zion. His information proves correct, and Zion/commando forces easily clean out an entire building of exiles with their new weaponry.
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