Hi Jason,
I think you're misunderstanding the meaning of the word "immigration". To go through immigration means that you're entering or exiting another country.
When you go through immigration, you present your passport, and sometimes you are asked questions like "How long are you staying in our country, and what is the purpose of your stay?", and if you are granted entry, maybe the personnel will say, "Welcome to our country."
For example, Singapore and Japan are two different countries. When a person comes from Singapore to Narita Airport, that person needs to "go through immigration at Narita" to "enter Japan", regardless of nationality.
Then, if that person wants to leave Japan, the person "goes through immigration" to "leave Japan", regardless of nationality, destination or port.
If you are coming from Singapore, you need to go through immigration to enter Japan. If you are "on transit" at Narita, you go through immigration and enter Japan at Chitose. If you are not "on transit" at Narita, you go through immigration and enter Japan at Narita.
But Narita and Chitose are both Japan. If you go through immigration and enter Japan at Narita, you don't go through immigration to go to Chitose. You don't go through immigration again until you're leaving Japan. You go through immigration again when returning to Singapore, or when leaving for another country such as China or Korea or the United States. But nobody goes through immigration to travel from Narita to Chitose, because the two cities are both inside the same country.
I thought that maybe you were asking, "Do I need to pick up my baggage when I arrive at Narita, and then checking in my baggage at Narita to go to Chitose?"
If so, it depends on how your ticket is issued. You need to ask that question to the place you bought your ticket, or to your airline. However, if you don't "check in" baggage, and bring all your baggage to your seat, then there would be no baggage to pick up or check in. Please keep in mind that you could only bring in a small baggage to your seat. Details on size are written on your airline's official website.
Lastly, your boarding pass for Chitose would be given to you at either Singapore or Narita, depending on how your ticket is issued.
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