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Step By Step Instructions | Tips for Players | Matrix Simplified Approach | Tips for entering the Matrix | Missions
"Your true mission is the utter and complete destruction of the Matrix."
"By our past are we defined.
By our actions are we molded.
By our legacies are we remembered."
"The past is the past. But in the Matrix, every moment--every move--every thought--
is stored...somewhere in the program."
Mission One: Go with Binary to the secret location researching the Matrix. It was deserted. Binary was kidnapped by agents. The research codes were recovered and uploaded to the Hyperion. They provide information and codes to download various things into the Matrix (such as your weapons) and secret information, as well as details about Zero-One and the Agents. The names of the researchers planning to escape were discovered. (The other researchers are presumed to have been killed by Agents.)
Mission Two: The party (in the real world) tries to rescue four of the researchers who escaped while X tries to decode the recovered files. Two of the researchers are killed, but Sam and Elle are rescued. A strange mutant creature's corpse (with the ability to repel the Sentinels) is also brought aboard for further study. Sam switches ships to go tell Zion all he knows. Elle stays behind to help with the decoding.
Mission Three: Unfortunately, the code's scrambling algorithms were through partitioned locks, meaning the writer of the scrambling algorithms can decode it. However, Vincent Giovanni wrote what he called the unbreakable code, so his help is needed to break the last part of the code. He was a master of recoding the Matrix and very eccentric and a bit of a misanthrope -- called a genius more than Stephen Hawking, and also in a wheelchair.
Although Vincent locked himself in his own recoded "Digital Fortress," the researchers decided they always needed a chain so that the code would not be lost forever. The characters have followed this chain to get into Digital Fortress.
Mike (aka "Binary") was a close friend of Vincent, perhaps because they were both eccentric. Vincent supposedly knows where all the major Zero-One hubs are and may be able to tap into the Matrix and help locate where Binary was taken.