According to Hiro, Lagos figured out all this, and after he'd put together the puzzle pieces about the ancient neurolinguistic stuff, he looked for someone to buy it.
Rife was interested. Lagos probably thought he'd sell Rife the intel and help him develop a technology that would help Mr. Paranoid Businessman keep control of the information that passed through his programmers' brains.
But Rife took the idea and went big. He poured money into archaeology, Christian evangelists, and drugs, and that's how the virus ended up getting passed on in human blood. Thanks, Rife.
The virus got passed to a lot of Third World folks through vaccinations that were purposefully contaminated, and Rife's Raft, in picking up refugees from all over the Pacific, helped gather them.
He figured out how to graft radio wires into people's brains so that they could directly receive his instructions—his me—and they could control the masses.
How did the virus get into binary/computer form? Hiro suspects that it was picked up in a radio signal from outer space, since the metavirus exists everywhere life does.
There are basically two types of people out there: the information elite (like programmers) and everyone else. Since hackers have learned to think in binary by learning to code, the binary virus will damage their brains, like with Da5id; everyone else can be infected with the regular virus.
Rife's beef with hackers is that he needs them to write programs and stuff, but he doesn't trust them and can't control them—hence having Snow Crash to intimidate them into submitting to his will.
Hiro thinks that the nam-shub of Enki is an antidote to Rife's religious virus. It's in that clay envelope from Eridu that Rife's university dug up.
Since Rife is probably using short-range radio signals to control his wired goons, Hiro needs to transmit the nam-shub of Enki to them pronto, before the Raft breaks up and hordes of mind-controlled refugees descend on California shores.
So Hiro's goal is to steal the nam-shub from Rife before all this goes down; the others say they'll try to send help, but obviously the Raft's core is really fortified.
Ng gives Hiro a newer, less buggy version of the software that runs Reason, too. We have a feeling Hiro will need it.