Formation History of the Japanese Islands
16 to 11 million years ago (Middle Miocene)
Fig. 5 Middle Miocene paleogeographic map 
Northeast Japan was broadly covered with the sea between 17 and 9
million years ago. A region from Akita to Niigata (the continental side
of northeastern Honshu) and the Ou Range were long and narrow basins.
The basin of the current Ou Range area was deepest in the beginning of
the Middle Miocene. Submarine volcanic activity was active in the basin
of the Ou Range area but inactive in the Akita-Niigata basin in which
thick deposits were formed. The Tertiary formations in this region
produce a little petroleum. The submergence of northeast Japan is
accounted for which the expansion of the Sea of Japan stretched and
thinned the crust to reduce its buoyancy and east-west tension was on
the island arc for a long period.
In southwest Japan, the sea expanded into western Honshu (Chugoku Region) to central Honshu during the formation of the Sea of Japan. The inland became archipelagic because of the relief. Subsequently, southwest Japan tended to emerge on the whole through into the Middle Miocene since this region was compressed by the subduction of the Shikoku Basin under southwest Japan resulting from the rotation during the expansion of the Sea of Japan.
Volcanic activity occurred in Kyushu, Shikoku, and the south Kii Peninsula through the southern part of the central Honshu (Kanto) in a short period about 15 million years ago. A very young and hot plate, the Philippine Sea Plate (Shikoku Basin) subducted and melted under southwest Japan, which caused this volcanism. The volcanic zone was closer to the Nankai Trough than the present volcanic zone. The volcanic activity differed from common activity in the arc-trench system (see "Volcanoes"). It is known that basaltic magma actively intruded into the Shikoku Basin.
In Hokkaido, the Kitami Mountains abruptly uplifted and a sea area with a deep trough that developed parallel to the west of the mountains in the middle of the Middle Miocene. The Kuril Arc began to collide with the Northeast Japan Arc in the end of the Middle Miocene (10 million years ago). This collision raised the Hidaka Mountains, which were a shallow-sea area, and the Yubari Mountains.
The Izu-Bonin Arc moved and collided with Honshu by the northwestward movement of the Philippine Sea Plate 15 million years ago. Blocks on the Izu-Bonin Arc accreted to the Northeast Japan Arc as they could not subside. The Misaka Mountains to the north of Mt. Fuji were a block on this island arc. Afterward, blocks on the island arc continuously collided and accreted to Honshu.
11 to 2 million years ago (Late Miocene - Pliocene)
Fig. 6 Pliocene paleogeographic map 
The volcanic front and the trenches were situated near the present
positions and the shoreline was similar to the modern line in this
period. The Japanese Islands, except for a few areas including
Beppu-Shimabara Graben, have been dominated by compression owing to the
subduction of the Pacific Plate and the Philippine Sea Plate since this
period. As a result, reverse or strike-slip faulting and folding formed
mountain ridges and basins. The active island-arc volcanism occurred;
in northeastern Honshu and Hokkaido, eruptions with large scale
pyroclastic flow produced volcanoes with a caldera, and in Kyushu,
grabens developed in the Hohi volcanic zone (on the north of the
Beppu-Shimabara Graben), which may be regarded as the pre-subsidence of
the Okinawa Trough extending to the southwest of these grabens.
In northeast Japan, the Ou Range began uplifting 10 million years ago and grew to mountains six million years ago. Since the uplift rate increased in the Late Pliocene, depression areas in the Miocene have inversely changed into heights. The mountain areas (Dewa Mountains) on the west of the Ou Range upheaved above the sea level 2.5 million years ago (Late Pliocene).
In southwest Japan, tectonic movement was milder compared to northeast Japan. Gentle warping occurred in the island arc direction in the inland five million years ago. Lacustrine and fluvial deposits accumulated in depression areas formed by this warping. The developed depression area resulted in the Seto Inland Sea. Neogene deposits except shallow-marine sediment of the Middle Miocene are hardly found in northern and central Kyushu. Therefore, Kyushu is thought to have been broadly land in this period. In the Nansei Islands, the Okinawa Trough began to be formed in the Late Miocene-Pliocene (or 10 million years ago).
In central Honshu, the collision of the Izu-Bonin Arc, which started 15 million years ago, still continued. The Tanzawa block and the Izu block accreted to the Honshu island to be the Tanzawa Mountains eight million years ago and the Izu Peninsula 1.5 million years ago, respectively. These multiple collision of the blocks markedly deformed the Honshu island, bended geotectonic structure such as the Shimanto Belt, the Chichibu Belt, and the Median Tectonic Line. The collision also effected on major configuration including the Akaishi, the Kiso, and the Hida Ranges to the west of the collision zone.
2 million years ago to the present (Quaternary) and future
Fig. 7 Pleistocene paleogeographic map 
The Japanese Islands has been strongly compressed by the
eastward movement of the sea floor of the Sea of Japan as well as the
westward subduction of the Pacific Plate and the Philippine Sea Plate since
two million years ago. The uplift rates of mountain ranges formed
between the end of the Miocene and the Pliocene increased because of
this powerful compression. As a result, an abundance of clastic material
from mountains was provided in lowlands. There are also considerably
subsiding areas. The Kanto Plain, for example, has sunk over 1000 m in
the Quaternary, being the largest plain in Japan. The uplift rates of
mountains in northern and central Honshu (Tohoku and Chubu Regions) are
greater than those in western Honshu (Chugoku Region).
The earth repeatedly experienced ice ages in the Quaternary. The Japanese Islands were connected with the continent by land during the last ice age (tens of thousands to 10000 years ago) because the sea level fell by 120 m. Mammoths came to Hokkaido from Siberia, and various animals came and went between southwest Japan and the Korean Peninsula. Glaciers developed in high mountain areas of Hokkaido to central Honshu, forming glacial landforms. Some of them remain in those areas.
Most Quaternary volcanoes are active in current positions and create characteristic landforms of the Japanese volcanic islands.
[In the future]
It is predicted that Australia will collide with the Asian continent about 50 million years later and the North American continent will meet with the Asian continent 200 million years later, based on the motion of the present continents. As a result, a supercontinent will be formed and the Pacific Ocean will be closed. The Japanese Islands will disappear because they assimilate with the supercontinent.
*Titles of the following references
[Pre-Cambrian - Cretaceous]
Isozaki et al., 2010 (in English)
Kanagawa Prefectural Museum of Natural History, 2010
[Paleogene - Quaternary]
Yonekura et al., 2001
Iijima and Tada, 1990