[Sangetsu]

Filipinos have the hardest time when it comes to getting a visa for Japan. You need to get her a military ID, then she shouldn't require a visa, but to get the military ID she will likely have to come to Japan on a tourist visa and apply for/receive the ID at your base. As for what happens next, I'm not sure, she might have to leave before the tourist visa expires and then return using her military ID card.