The news about the aircraft this month has been special, not just for the fact that a Zero has been flown/flying over Japan (which is not the first time since WWII), but that a Japanese-born pilot has been at the controls, which is a first since WWII. As I recall, the owner of this particular Zero, Masahide Ishizuka, had the goal in mind of having a Japanese pilot flying a Japanese WWII aircraft, such as the Zero, over Japan, to help inspire a drive to build a larger/stronger aviation industry in Japan, as there was during/before WWII. The Japanese-born pilot that has been flying the aircraft, Kazuaki Yanagida, is a California resident and highly experienced flight instructor. This particular Zero was flown over Japan back in January 2016, by Skip Holm, but since then it was shipped back to the US and Yanagida got checked out in the aircraft at Chino, CA this past spring, before the aircraft was shipped back to Japan. Ishizuka has had a troublesome time, facing various hurdles for several years now, trying to get the Zero on the civil aviation registration in Japan, but he has finally settled on keeping it on the American FAA registration. I recall it took a long time in Germany too, before they began more widely accepting WWII-era fighters/warbirds on the civil register there, finally largely due to the efforts of MeierMotors.
This particular Zero, an A6M3, was one of three that were built-up as "restorations"/reproductions in Russia in the 90's, using limited original parts, original drawings, original identities from recovered wrecks, and R-1830 engines (essentially identical in specs to the Japanese Sakae engine). This particular example first flew in 1999, as I recall, and spent many years based at the Mojave airport - as a result, it was usually referred to as "The Mojave Zero".
The aircraft is one of five airworthy Zero's - this includes Paul Allen's/FHCAM's A6M3, the Commemorative Air Force SoCal Wing's A6M3, Ishizuka's A6M3, the Planes of Fame's A6M5 (the only one with original engine), and the Texas Flying Legends A6M2 (repairs and upgrades are completed and it will be flying again within the next few weeks, in-time for Oshkosh). A 6th flying Zero is nearing completion at Legend Flyers, quite possibly to fly by the end of the year.