Warning: this gets kind of dark.
Despite being a weaboo with only secondhand knowledge on Japan, I've kicked around some ideas over the years for what Japan as a whole has become in the city of heroes universe, particularly as my live namesake was a 'too old' magical girl brought out of retirement and a traumatized Rikti War veteran. I don't have a specific zone in mind (I had a pitch on the live forums for a trio of zones, one hero, one villain, one neutral) which were purely ficticious locations, more recently I thought about Urayasu in the Chiba Prefecture in the Tokyo Bay since that area does have this stark divide of 'the traditional Japanese settlement Circa Tokugawa Shogunate' and 'Shin-Urayasu' which is expressly a modern area and includes the freaking Tokyo Disney park. But the general ideas I've had were:
Japan outwardly presents itself as 'Animeland' and it's not far off from the truth, the JDSF remains on high alert since the Rikti War and have cooperated with the Vanguard making extensive useage of salvaged and reverse Engineered Rikti assault suits creating a mecha-nized national defense force, there's government trained mages who are inducted from an early age when they show potential and at taught in specialized occult schools in places like Mt. Osore.
The hero scene in Japan, in truth, is highly bureaucratic and commercialized (think a cross between One Punch Man and Tiger and Bunny) in which even a hero capable of fighting off certain crimes will be forbidden due to it not matching their public image as well as it simply not being what they're registered to do. This in part was started due to metahuman warriors and even full lords of the the Sengoku and Edo period causing flareups in power discrepancies and civil unrest and by Meiji the Emperor sought to keep better control on these individuals, further compounded by WWII surrender agreements which brought the Super Hero Registration act to Japan and brought a hard cap on how many registered heroes were allowed to be active. Unlike the limits on Japan's military, the 'legal hero' limit would remain in place until the Rikti War.
This, along with various injustices in the Japanese Justice System (IRL reference point: Japan has a 98% conviction rate and judges have confessed to knowingly convicting innocent people to save face of the system, crime in general is also not 'non-existent' so much as under reported due to societal pressures and police not wanting to bother) have led to a rise in Japanese Vigilantes who dub themselves 'Shin-Ronin' (New Floating Men) and operate outside the system to dispense justice as necessary. They're often reviled by the Japanese populous at large and commonly associated with Yakuza (which for some isn't always baseless) and are publicly hunted by both local police, heroes, and JDSF. (in private many have their sympathizers whether to Shin-Ronin as a whole or individual vigilante heroes)
Despite this, many 'Shin-Ronin' are under trained, often minors, and suffer from a high mortality rate. As magic became a known weakness of the Rikti, it's estimated that young girls as young as 6 years old wielding basic magical powers were killed or captured en-masse by Rikti 'mage hunters' who could dispatch with these unprepared magi and were able to crush the more centralized hero agency of Japan at large.
However, Shin-Ronin both magical and otherwise proved indispensable in the Rikti War and restrictions on hero registration were (largely) lifted and heroic associations were (mildly) decentralized, and in other cases, public and government opinion softened on Shin-Ronin, both as a result of the Rikti War and their aid in situations such as dismantling the Yakuza and various disasters which racked the country and the world since the start of the 21st century.
Because of all this Japan is reluctant to accept the aid of non-Japanese heroes, though those that manage to break through the redtape and/or win over the populous are viewed with a certain awe and inspiration to the local heroes, though they are quick to try to talk to these foreigners in what is often mistaken as 'helpfulness' but rather is done in desperate attempts to avoid international incident or the high property damage western heroes are stereotyped as causing.
Rose Star is a registered Japanese hero and on the up and up, her partner Spark Blade however is a Shin-Ronin and perhaps one of the most well-known in Japan, which, to the consternation of authorities and even his partner, means he can avoid much of the Shin-Ronin stigma on pure popularity. Spark Blade avoids registering both because it would violate his own persona as a cool, loner-badass, but mainly because he genuinely dislikes the commercialized and regulated system that could stop him from helping others.
Mecha, piloting, and combat are done very carefully in Japan, with such heroes only being called into an urban area (or populated areas in general) if conventional hero forces are exhausted or if a 'kaiju class archvillain' has appeared within population centers with no forewarning. Engagements are urged to be taken away and dealt with outside these areas. Also regulations stipulate Mecha models are not allowed to be built higher than 7 meters (or 23 feet).
Enemies in the country
There are dark rumors circulating that hidden circles in the Japanese government is in cooperation with Malta.
Urban legends persist of independent 5th Column cells who sought sanctuary after the fall of Berlin or even settled in as early as Japan and Germany's initial alliance.
More rumors still haunt the country of a remnant faction of the Imperial Wind, and relatedly experiments of Unit 731 smuggled back to Japan and having subsequently broken loose, or the dark research continued.
Not all Shin-ronin are necessarily Heroes, sadly more than a few can best be summed as 'villains with a cause' and end up fueling public sentiment against vigilantes.
likewise, more than a few modern 'villains' seem to be nothing more than exaggerated performance arts actors who do wild and absurd stunts for attention, meeting their favorite heroes, and generally just to act out their (hopefully non-sexual) fetishes in public, at worst they might be petty bullies and thugs with a flamboyant streak. Naturally these types of 'villains' ended up dubbed as Chuunibyou. (Japanese authorities advise heroes deal with these people with a public unmasking and calling their parents or completely ignoring them, robbing them of their power.)
A lot of scientific disasters can, with deeper investigation, be traced to the Crey rival: Kasa Pharmaceuticals*.
Yes, there's also oni, other youkai (just not that weirdo that has an eye in it's butt)
And an obligatory J-horror mission
Oh, yes, can't forget the most important type of enemy to fight: SHOKAH~! (Or rather kind of kitchy and cheesy senair baddies.)
*Yes, it's a reference. Just count yourself lucky I didn't make it Orochi Corp.
So, it's a rough idea that could probably be focused down into a zone, my ideal would, again be making a zone where there's that divide between the new and the old. Heroes would probably be brought in as 'Shin-Ronin' by Spark Blade to help with maybe the Fifth Column ("primarily a Paragon problem") then a storyline would continue to reveal the various forces tugging at Japan. The options of the story would focus on whether you would deal with these threats yourself, opening Japan up to the idea foreign aide better or merely serve as a guide to help the Japanese people fight against these threats on their own, encouraging independence. Villains meanwhile would be brought in to assist a remnant of the Yakuza (which you would have the option to betray and take over/wipe out) and build them back up by corrupting Shin-Ronin into a life of full crime and disrupting Japanese Authorities, ultimately culminating to robbing either a warehouse of JDSF Mechs/Drones (either to keep for yourself or unleash on the populous) or going on a heist to steal one of the Imperial Regalia, specifically the Sword of Kusanagi. (Either to keep for yourself or force the Japanese government to pay up).
man, I came up with those storyline synopsis on the fly, but I kind of like the choices I managed to give to them. I do admit that maybe this all seems like I'm being a little too hard on Japan as a country, but it made for some great trauma sources for my magical girl back in the day.