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- For the reports of alien sightings and abductions in the Matrix, see Ethereal.
Aliens were beings of unknown origin. During the Machine-occupation of Earth and during the course of centuries, the Machines sent probes to space. The aliens must have been tracking them with the help of one of these.
A ship arrived close to earth with tendrils which hurled asteroids to Earth. One such asteroid took out a central processing unit, and 200,000 humans died from the Matrix but the Machines had a mirror going. One of the bluepills found himself floating in a vacuum for a couple of nanoseconds, while London returned to processing again. During this experience, he met a program, perhaps an Agent, who explained to him what happened.
For the next twenty minutes the Machines worked to get a retaliatory plan up and running against the alien ship and the Matrix ran in an accelerated mode trying to patch and cover up the loss of time. Seventeen minutes later, that individual thought that years had passed, until he had the same experience with that program. Then he had a redpill experience and saw the pod he was in.
Sometime later the Machines decided to reset the recent history of the matrix and the individual was chosen to re-live his life but this time trained as a RAF cadet. When his training was complete, he woke up in his pod and was taken outside into a PL-47 prototype. He left Earth and attacked the alien ship, and was victorious.
However the Machines did not bother to have him return back to Earth, only reconnecting him to the Matrix as a final wish.
The physical appearance of the alien beings was unknown; they likely had some type of knowledge of or disdain for machine intelligences, as all of their technology, including their space ship, was organic. The ship was said to have resembled a fungus or plant.