Okay, the very dumbed down story so far for those of us just joining.
69086 AURORA CYGNUS is an AI placed in charge of the Coventus Facility. Another AI has hacked into AC's mainframe, and has either locked him away or has destroyed him. This AI then shut down the Facilities defenses and found something that it didn't know was there. What this is, we aren't sure. It could be anything from another AI to a Gravemind. This AI seems familiar with the Coventus Facility, so may have been an AI placed in charge before AC was, or may be an AI who was once "on the same side" as AC.
That's the story in layman's terms.