Fallout: Tokyo takes place in and around the great city of Tokyo approximately 100 years after the Great War.
Due to atomic testing in the Pacific during the 1950s, atomic monsters emerged to plague Japan, preventing the country from industrializing and becoming the Asian Wonder. The country used all its resources just to keep the kaiju at bay, so the Chinese just didn't bother conquering them. When the Great War came, Japan suffered less than its neighbors, being a tertiary target, and quite possibly have rebuilt the world, but the radiation multiplied the atomic monsters, laying Tokyo low.
Pre-war, the job of defending Japan fell to the Nippon Science Team, its own branch of the military, tasked with developing and deploying weapons capable of defeating the Kaiju. To defeat the small kaiju, they developed the first suit of power armor, the technology of which was stolen by US companies. Later, they took that technology to develop gigantic suits of power armor to challenge the largest kaiju: the M-01, M-02, M-03, and the brilliant but uncompleted M-04.
During their defenses, the Science Team discovered that there was a force driving the kaiju, something artificial pushing them towards Japan: the Zetans, secretly plotting their conquest. Using altered human agents, they infiltrated the government, but this plan never came to fruition, for the bombs fell. The Zetans lost their control of the kaiju, and afterwards, only controlled very few of these creatures.
The Zetans want Tokyo as its the perfect base to launch a worldwide assault. After the bombs dropped, the Zetans on the ground have lost contact with the Zetans in the mothership. They've built a number of craft in an effort to reach the mothership, but each ship crashed before they could reach their destination.
After the Great War, the wards of Tokyo split apart, divided between Yakuza criminals who eternally war against each other. These gangs demand the utmost loyalty of its members, and all defer to their bosses, until they can murder him at take over themselves. Meanwhile, the Japanese Defense Force (JDF) had also survived the war, seeking to fight the raiders. However, they don't trust the Science Team. Despite many promises, the Science Team isn't able to keep a mecha in the field, and so the generals of the JDF have written off that faction, but are unable to find their hidden base.
The city is a mixture of traditional Japanese, European colonial, and modern architecture. While the US culture stopped in the 50's, the Japanese stopped in the mid-60's, preserving their fashion of skinny ties, mini-skirts, and go-go boots, while also preserving their kimonos and katanas.
Notable landmarks include Asakusa, Tokyo Central Railway Station, Tokyo National Museum, Tokyo Airport, the Imperial Palace, University of Tokyo, National Diet Building, the Kabuki-za Theatre, and the sea port.
The Science Team did its best to defend the city, buts is battle suits slowly broke down. At this point, even the M-01 is out of commission, as they've been sacrificing everything to complete the M-04. Their only problem is that the original pilot of the M-04 was killed during the war, but his brainwaves are already imprinted on the computer controls. In order to make this machine operational, they've cloned the original pilot, raising it to maturity in a vat.
Weeks before the clone was ready, before it could finish its machine learning, the cloning facility was attack by the Zetans, killing all the scientists, and released the clone prematurely. The tracking beacon that they surgically placed into the clone in tells them that it's still alive, but where? Somewhere in Tokyo.
You play as the clone, awaked in battle, witness to the wrath of a kaiju, barely escaping with your life into a city where you can't even read the signs, in an eternal struggle to survive.