The reason Shadowspire are targeting A.R.G.U.S., and Amanda Waller gets killed, is because they want to get their hands on something called Rubicon. Waller is happy to have everyone die rather than give it up, and Lyla only starts working on the access codes when there's a gun to John's head, stating that they cannot allow it to be released. So, obviously it's something pretty major, and devastating. But, er, what exactly is it? The name alone implies it's something that there is no coming back from, but that doesn't help us understand its nature. Is it some sort of weapon or virus? Or is it some sort of incredibly damaging data? Something else entirely? Hopefully, despite Shadowspire being defeated, we will get to find out.