It all begins when Netto's (Lan's) father invites he and his friends to see the first test of cross fusion. This technology allows the user to become one with their PET (PErsonal Terminal) and net navi in the real world via what is called a synchro chip. (For the uninitiated, net navis are inside the PETs and handle things like mail and virus busting. Everyone in the EXE/Battle Network world has one.) However the original tester couldn't hold the fusion for very long as the process is very draining physically, usually resulting in feeling very weak or passing out afterward.
After the test, the lab's system is taken over by viruses and a navi known as beast man. Rockman manages to defeat beast man in the virtual world. However it doesn't end there. The enemy sends some sort of device down to Earth and a dome called a dimensional area surrounds the lab. The viruses that once plagued the net world have now entered the real world! Against his father's wishes, Netto decides to give the synchro chip a shot and manages to send the enemy on the run, including beast man.
All in all this looks like a very promising series. I wonder what happens to the operator of a cross fused navi should s/he be deleted? Do they die? Not sure if the writers are even gonna go into that. This whole "real world meets net world" concept reminds me of a certain PowerMan 5000 song.