GM Explanation: Here's a synthesis of the information, since it takes so long to get it out on RPoL:
BUGS IN THE SYSTEM
The Matrix in its native state is a creature that can infect the machines, as it did when it attacked you. (It is highly susceptible to extreme heat and thrives in cold.)
You discovered that the Matrix is part of some sort of scientific effort to control and use it for something. This is some sort of secret research through ByChem. (This is not relevant to how it got out of hand back in the previous adventure; that was the Matrix in its natural state.)
You found the datastick (now held by Shinsa) with the downloaded information and, presumably, an isolated version of the Matrix.
This message was decoded from the datastick, with Shinsa attempting to decode more:
Accessing alien datapad...
Mass file corruption detected...files deleted...
#&$(##~contact Ky*#&!)#n at ByChem for anal#*$&! Venturi*#&!*!#(@~
#*$(#&!~catalyst detect&#(*$~)(@%%Jetsom infection caus#&$&#~)#(!@#
(!*&$Matrix succes&~(!@*#@control#(!!)~!@collateral damag#%*@body co#
deaths inconsequent@!%$%#$&*#~#Akizk must die#*&@(#crew eliminat##*!(@
#~!&#(#bio-chemicals needed$&##*!)!invasion imminent$#*!new race$*#!
code nam#&@Shadow&#Rakon.#&*!#$*#####!(#$~$@($*@~$@~$&%!)*$@(*!@*~
@)($%
Alien messag#*($&**!(. Following decod&# and translat#@:
&*$ the stars carry this mess#&$*# of &#*$#!%
Heretics accord$#*#%# Qantariate&$#@!%#&*#@(!
Symbol of #*&$#&~)@$(##@!~(~%#%^#@%!to death@$
#&*(!@#&*will arrive in#*!%)#*(cycles*#&%#$#@
THE BLACKNESS
You discovered in this adventure that there is a species of extra-dimensional aliens that can pop into this dimension -- the Qantariate. One of them seemed willing to aid you and gave you the datasphere. Unfortunately, the vast majority seem to have aligned with the Sathar for some unknown purpose. They can use tracers to get to certain locations (but none are on the shuttle, luckily). The Qantariate members who oppose the Sathar are called the Synth.
Apparently, the ByChem experiment with the Matrix was to try to use them against this potential alien invasion threat.
You now have the datastick, which is more fully decoded now, but the alien datasphere, if given to the right person, can be used to fully decode all the data on the datastick:
The Qantariate are trying hard to get the datasphere back from you.
Kyrillian told you: "The Matrix Project was formed to use the Matrix virus against some sort of invasion by extra-dimensional creatures. It was thought their broadcasts and transports could be interrupted by inserting the Matrix virus. Kyrtok and I were charged with experimenting with the blackness they use for transport. Somehow, they tracked us here."
Kyrillian also translated a message from the now dead Kyrian to the now dead Kyrtok:
"I am told that getting the machine to work will bring a datapad or artifact to us that will allow us to decode the alien messages received on Moneyspider through the Matrix Hole Between Worlds. The Qantariate discovered our universe because of the Matrix. I think it should be destroyed but the Synths believe it is critical to our success in preventing an invasion that will destroy our universe more surely than an antimatter annihilation.
The artifact can be taken to Tariel Nuna on Kraatar, who knows about the Shadows of Rakon and is best suited to figure out what it means. We should also get Dr. Legrange involved. He's brilliant.
I have decoded the "cycles" listed by the aliens. Each cycle is the equivalent of 1 month. This means we have less than 2 cycles left before the invasion! I'm in a panic. The worm creatures are involved too. How, I don't know, but somehow."
So apparently the Synth also believe the Matrix is critical to preventing the invasion.