WARNING: SPOILERS AHEAD
My understanding is that Thorne was security chief at Encom. He found out that Alan Bradley re-discovered the technology to digitize and store a human being in a computer. Apparently, when the MCP was destroyed, that technology was lost.
Thorne stole Alan's work and showed it to a competing company, fCon. In order to prove that it worked, Thorne used the process on himself. Unfortunately, Alan hadn't quite perfected the process yet. So when Thorne was digitized, he became corrupted. It's driven him mad, and now he's on a crusade to take over the entire electronic world.
Thorne has become like a god, and he's spreading his infection and influence to every program he comes in contact with. He's also infecting the system surroundings themselves, in the fCon mainframe. So, in effect, Thorne has become a virus. If he isn't stopped, he'll eventually destroy the entire electronic world by spreading through networks, to every machine there is.
Because of what happened to Thorne, fCon first tries a hostile takeover of Encom, and then finally kidnaps Alan, in order to find out how to make the digitization process work correctly. As it turns out, Alan has found a way. So fCon then sends in more people, who become the Data Wraiths. Their job is to take over everything in the electronic world, in the name of fCon. They want to stop Thorne, and then manipulate the system to gain fortune and power.
So that's where Jet comes in. He gets pulled into the electronic world against his will by MA3A, and is asked to help stop Thorne and the Wraiths.