The three Endpoints refer to three islands in the New World which seals a huge amount of subterranean magma. Should all three islands be destroyed, the seal will be undone, releasing enough magma to wash the entire world in molten rocks.
Due to the hazardous potential, the World Government hid the Endpoints' existence, creating cover-up stories, so only the highest ranking of the Government; Sengoku, Garp and Z knew about their existence before Z's plan intertwine with the Straw Hat Pirates. Under the encouragement of the Government, the worldly masses dismiss the Endpoints as myths and legends.
One Piece Film: ZEdit
Wishing to put an end to the Great Age of Pirates by destroying the three Endpoints, Z steals the Dyna Stones from a Marine Base on Firs Island; an Endpoint itself. During his first fight against Kizaru, Z uses a Dyna Stone to destroy the island.