Maybe the government doesn't know who the target is, they just know that there is a target, which probably makes them all the more nervous because what if that target is them? Meanwhile, W&H remains completely oblivious. And a lot of tension regarding the hacking is to keep them oblivious. Then in the climactic scene, the sentient system becomes aware but the virus successfully deletes that knowledge.

Or blackmails the system, I suppose. If it's self-aware then it must have personality and weaknesses.

Then the sequel:

Dealing with a semi-evil sentient computer system that knows more than is healthy for you but has refrained, so far, from spilling your secrets to its masters. Or at least, if it has told, they're holding off on acting on it. Very unclear motivations regarding the computer program.

(Maybe Methos wrote it? Heh.)

Back to the original story, though, Riley and Slayer HQ could provide job offer and counter offer and the hackers could try to get the best deal. Because, while Slayer HQ may have a definite coolness factor, what they don't have are the amount of funding that the US Army has or the respectable reputation that parents might like in their kids' jobs.

Anyway, this would be a very cool story. Somebody (not me) should write it.