Are you in Japan now?
If so, keep watching the English-language press for specials from travel agencies. There are a lot of consolidators there.
Otherwise, if you are in a different country, see if you can arrange a flight from your home to Seoul with Tokyo as a stopover.
I know that when I took a trip that included Taiwan for a week and Japan for two months, my original intention was to go to Taiwan at the end (U.S. West Coast>NRT (stay for two months)>TPE (stay for a week)>U.S. West Coast), but my travel agent convinced me that it was significantly cheaper to go U.S. West Coast>NRT (stay overnight)>TPE (stay for a week)>NRT (stay for two months)>U.S. West Coast.
Back in the days when I was advising students for study abroad in Japan, they often found that it was cheaper to do a U-turn in Hong Kong (U.S. West Coast>NRT (change planes)>HKG>(spend a couple of days)>NRT (stay for a semester)> U.S. West Coast) than to just fly to Japan and stay there.
Play around with the routings from your home country. When I planned my last trip to Japan, it cost about 60% more to fly non-stop from MSP than it did to go MSP>LAX>NRT.