There are a great many pokemon who have gone extinct over the years, and a wide variety of causes for these extinctions are known to science. Some are quite common: a food source going extinct causing a chain reaction, being out-competed by new predators, or perishing in a global catastrophe. And then there are the Bastiodon, the only pokemon known to science to have been literally wiped out by an earthquake.
Powerful earthquakes have been known to kill individual electric and fire types, and occasionally do likewise to rock or steel pokemon, although their tough defenses usually allow them to survive a single quake. Yet one megathrust earthquake and its intense aftershocks, in strata now found in ancient Sinnoh but believed to have been picked up by that vast Torterra island after the age of the Bastiodon had passed, has shown itself not only in damages to rocks. It has also appeared in the numerous toppled steel plates, many with large tusks sticking out of them, which had once been standing and live Bastiodon. Like large structures built by Man, Bastiodon were often toppled by earthquakes, for evolution had given them their strong defenses at the expense of their ability to resist natural disasters.
Tragically, the principles found in Bastiodon's iron bodies, and the difficulty in destroying or moving their corpses before explosions, led the people of ancient Sinnoh to conclude it an ideal shape for defense. Although Sinnoh is relatively free of earthquakes, not being on a tectonic plate, the Torterra itself can be shaken by the large calamities of the north pacific. And when that happened, the destruction was total; Sinnoh's first fortress civilization perished overnight.