Everyone imagines aliens to be sentient creatures with bodies, often interested in carrying off our women.
An alien electromagnetic field, resembling a computer virus, travelling between the stars. It encounters our cosmonauts and downloads itself into their cyberware (hence the blackout), the ship's computers, and similar devices. Slowly it spreads throughout the Matrix, not sentient (yet) but seeking to propogate. Matrix researchers find and isolate the strange code, studying it to find out what it is. And in the research, the alien gets concentrated enough, and access to enough processing power, to wake up. Now it follows its own agenda.