The intro movie implies that some sort of Vasari propulsion experiment is involved.
Perhaps they opened a phase lane to some other place, and accidentally drew the attention of some greater power. This power is now following them, consuming all worlds in its path.
The manual also indicates that the one warship that made contact with whatever is following the Vasari and survived to return had not only sustained serious damage, but also had its crew driven mad with fear.
Maybe they released some sort of imprisoned or trapped ancient race? Perhaps it is something that can posses others and/or snap a beings mind like a dry twig.
In that case, it may be the Advent's knowledge of psi-tech that is the key to stopping this.
As an aside, the concept of cybernetic vehicles (craft which utilize both mechanical and biological properties) is quite viable, and may simply be the inevitable result of technology as it grows more sophisticated rather than some strange alien thing. The recent incarnation of Battlestar Galactica (love it or hate it) presents a good example of how this technology might function. In the real world, our technology is gradually moving in this direction already. Early examples of human/machine integration can be seen in things like the
Emotiv products. In fact, one theory posits that we might not ever develop "AI", and instead may simply use our own minds to control machinery. It is not nearly so fictional as the concept of psionics, which has no known viable method of function (though I suppose it could be discovered one day,
if it even exists).
