So your visa is expiring soon, and you need to renew your visa aka get it extended. If you live in Tokyo, you will most likely have to go to the Shinagawa Immigration Center.
How to get there and what to do
First, get to the Shinagawa Station
If there is a line outside, join the queue and wait for your turn to get in.
Once you are in the building, head up the escalator to the 2nd floor and join the queue. The counters are right in front of the escalator.
This is where the staff will check your documents and inform you if anything needs to be changed or if additional documents are required. They will then hand you a number and direct you to the next set of counters where you will then wait your turn to submit your documents.
Once everything is done, you are free to go and enjoy the rest of your day.
The Shinagawa Immigration office can get very very busy, so sometimes it is better to get there either early in the morning or later in the afternoon.
Additional information and links
Opening hours and phone number