What kind of visa is naturalization?
We're only going to cover the most common case here for visas, as there are hundreds of combinations and cases and special rules for every circumstance and focusing on visas or permanent residency is outside of the scope of this site.
Permanent residency and special permanent residency in Japan, by the way, are also not "visas" — as you can't get them overseas — or status of residences, even though they look like status of residency stamps in your passport and they're usually listed with the other statuses on immigration web sites. Permant residency is only obtainable once you have a status of residence in Japan. You can skip being a permanent resident on your way to naturalization.
Visas are almost always obtained overseas. Modern visas in Japan are usually stickers which take up an entire page of the passport and have your expected status of residence, length, and a photo on them.
At immigration, they will probably mark your visa as "used" and put another sticker in your visa that is about a quarter of the size of a passport page marking you as having a status of residence in Japan, a date of issue, an expiration date, and a QR 2-D bar code for quick scanning (the older stamps from the nineties used 1-D plain bar codes) by immigration computers and unmanned automatic gates. To keep the status from being canceled if you leave Japan during your residency period, you'll need to get a re-entry permit, which looks just like a status of residence (it has a QR code). They will scan that QR code every time you come in Japan to verify it with their databases.
A permanent residency sticker looks just like a residency sticker except it's usually a different color (gray these days) and it has no expiration date on it. It also has a QR code.
When you naturalize, the Ministry of Justice will automatically contact Immigration (which is a division of the MoJ) and have them cancel your re-entry permit and/or the permanent residency or status of residence stickers you have/had in your non-Japanese passport, so when they're scanned at immigration by computers, an error will occur — even if the expiration date hasn't passed and they have no "void" or "used" stamp on them.
Visas are almost always obtained overseas. Modern visas in Japan are usually stickers which take up an entire page of the passport and have your expected status of residence, length, and a photo on them.
At immigration, they will probably mark your visa as "used" and put another sticker in your visa that is about a quarter of the size of a passport page marking you as having a status of residence in Japan, a date of issue, an expiration date, and a QR 2-D bar code for quick scanning (the older stamps from the nineties used 1-D plain bar codes) by immigration computers and unmanned automatic gates. To keep the status from being canceled if you leave Japan during your residency period, you'll need to get a re-entry permit, which looks just like a status of residence (it has a QR code). They will scan that QR code every time you come in Japan to verify it with their databases.
A permanent residency sticker looks just like a residency sticker except it's usually a different color (gray these days) and it has no expiration date on it. It also has a QR code.
When you naturalize, the Ministry of Justice will automatically contact Immigration (which is a division of the MoJ) and have them cancel your re-entry permit and/or the permanent residency or status of residence stickers you have/had in your non-Japanese passport, so when they're scanned at immigration by computers, an error will occur — even if the expiration date hasn't passed and they have no "void" or "used" stamp on them.
