Great Age of Expansion
During the Kryptonian Expansion, scientists created many World Engines and used them to colonize many other planets. However, after their society's adoption of artificial population control, the colonies established were abandoned as they were no longer needed.
Reclaimation by the Sword of Rao
Following the destruction Krypton that resulted in their escape from the Phantom Zone, war criminal General Dru-Zod and his Sword of Rao insurgents searched through the abandoned colonies for other Kryptonians who may have survived the event. During their search, while visiting Daxam, the group came across a World Engine, as well as a number of dropships and weapons, and attached it to the newly purposed Black Zero.
After Kal-El activated the beacon in Scout Ship 0344, Zod followed the signal to the planet Earth, and decided to terraform it in order to help the Kryptonian race flourish once more, at the cost of killing mankind, so long as Krypton's legacy prevailed.
Determined to stop General Zod from carrying out humanity's genocide, Superman confronted the World Engine in the Southern Indian Ocean. Despite being weakened by the now-Kryptonian atmospherics surrounding the device, and battling both its defense systems and the gigantic gravitational beam being channeled through the Earth beneath it, Superman succeeded in destroying the device, flying upwards through its core, ending the terraforming process.
18 months after the World Engine's destruction, it's huge wreckage could still be seen in the Indian Ocean. Lex Luthor hired a team of divers to explore the underwater area that the Engine was once positioned above in hopes of recovering a portion of the seafloor had been terraformed into Kryptonite, a green, radioactive xenomineral capable of effectively weakening and depowering Kryptonians.