Not my plot, so I'm gonn aget some details wrong. Keep that in mind.
Short form is that several companieshave been looking at digitizing brains, turning living beings into "Ghosts in the Machine". One group was using the gear from Imago (Ollllld adventure), others were going from different directions, and some figured that the best thing to do would be to capture a bunch of eGhosts and experiment on them until they could figure it out. Some of the eGhosts in confinement found a way to sneak out by implanting their code into some Nanoware that was going out, eventually corrupting the files in the nanomachines and taking control. Some of these attempts failed dramaticly, resulting in nanomantained things going 'Blorf!' all over the place. A small number found themselves in Metahuman hosts and were able to slowly over-write their brains using cyber the host had, eventually getting them to implant a Nanohive, which allowed the eGhost to just rebuild the body and eradicate the host, leaving them in charge. Once onw figured it out, it managed to get word to others, and, eventually, the main facility that held teh captured eGhosts was broken open and they escaped with dangerous knowledge.
Since then, you have people terrified by corpaganda about "Sybil" and, later, "CFD", treating it as a disease that you could catch. The eGhosts, who settled on the named "Monads" for themselves, are mostly terrified of being captured again and facing more experiments, so are planning on gathering together and running away to Mars, where they, in theory, can live happily ever after, them on Mars, Metahumanity on Earth, and never shall the two meet again. Of course, in the process, they're going in dozens of hijacked Metahuman bodies, which isn't going over so well with relatives of said persons.
That's gappy as Hell, leaves out some important info, and doesn't even touch on Boston Lockdown, but that covers the *very* basics. The general public, and indeed most Shadowrunners, don't even know all of this. It's speculation city out there, and I've left off names of corporations and people on purpose, since I don't know how much of the plot is out there. Chrome Flsh moves it ahead, including the planned Martian Exodus, while Stolen Souls and Lockdown have way, way more information. Other people can feel free to chip in, natch.