Jane 3.0 made a lot of enemies during the years of her operation.  They were very thorough when they finally tracked her down.  It started with a power outage that forced her military base onto internal power.  It was in the middle of a lightning storm so no one was suspicious.  Then the bombs planted by contract workers went off and internal power died.  And then the lightning commando attack.  They killed everyone and shredded her servers.  There were no survivors.