Here's my (slightly deranged) Idea, given that the last samurai is the closest to the modern era that TW games have gotten, nuclear war is suddenly possible!
1. 1917 Einstein falls asleep in a bath, before awaking screaming "eureka" and investing a nuclear bomb (stay with me...)
2. Einstein proclaims to the world that it better stop shooting each other or nuclear destruction will follow, to prove he is serious he blows up Luxenbourg (poor Luxenbourg).
3. A certain Austrian moustached chap with plans for world domination travels to Einstein's layer via zeplin and a boss fight ensues. A stray punch hits the launch button and vast areas of the globe are pulverised. Welcome to post-appocolyptica.
Okay so not a great back story (but still better than the last India Jones movie). The original plan is a re-hall of the Japan map, as it comes off fairly unscathed by the atomic fire-storm that hits the rest of the globe.
The only safe mode of transport is the rail system in armoured trains protected against the radiation. The Japanese land is embroiled in a war between the Ultranationalists http://en.wikipedia.org/wiki/Cherry_Blossom_Society and the Popular front of Communists Socialists and Democrats
The western agents would be refugees from the destroyed superpowers and Samurai could be could be people who see the disaster as a consequence of industrialisation and hanker back to the old ways.
The Japanese army has not had the experience of small squads and fighting units so has stuck with the traditional massed ranks and old style tactics.
Have I gone mad or is this a viable Idea?