You're better off just turning yourself in at the local immigration office and saying that you want to leave - you will be able to come back in a year and no record will be kept of your overstaying.
The best part is, while they are doing their paperwork, you can go home for a week, watch NHK and pound some lemurs you lured back with your sob story of "They're making me Leaaave!" until they serve up your voluntary deportation notice.
OFC if you have some compelling reason to stay in Japan (halfu kids) or have being overstaying for an exceptionally long time (~decades), you can apply for a special visa.
They will try to convince you take the voluntary deportation, but if you insist that you want to stay, then you just have to avoid getting arrested for about 8 months and you will be legal again.
