The way it’s theorized in GitS (which by now you should realize I have a very strong favoritism for) is simple nanobots that are just about as good, or slightly better than a human neuron, but about the size of a bacteria.
They get injected into your arm, make their way into the brain, and find an organic buddy to copy. You end up with your brain enmeshed with a network of much smaller robotic neurons, that copy the meat guys for awhile, then eventually you offload more and more to the silicon until eventually, you’re so old all that’s left is the silicon.
And in the process you get some awesome powers like synthetic telepathy, and device drivers for prosthetic bodyparts, and REAL GODDAMN MEMORY that doesn’t fade or corrupt from the same things human memories do. You also get all the benefits of just doing what computers do.
But GitS is a lot like I, Robot. It looks for the problems. Like people of sufficient skill finding vulnerability in your cyberbrain, rewriting all your memories and turning a bunch of upstanding citizens who’ve read a very specific account of a certain rebellion into mindcontrolled assassins.
Or cyberbrain sclerosis where a part of the population reacts badly to it, and end up with neurodegenerative diseases.
Or “closed shell syndrome” which is basically cyberpunk autism. People who take to it so well and so rapidly that they shut themselves off from the world to keep themselves from hurting other people with their godlike powers.