An evil sorcerer by the name of Skippy was formulating his evil plot. Well, to be fair, he was now more than just an evil sorcerer. Years at Munich Academic Department's School of Science had paid off and he received his PhD in applied theoretical quantum physics. He was now a MAD scientist.
And, again, to be fair, his plot wasn't all that evil. Sure, his previous attempts at alchemy were aimed at destroying the world. Yeah, he invented Tang through said alchemy. But he had left those days behind him. He was now working for the better of the planet.
It just so happens that he had a plan to allow the planet to heal as it should. To develop as it should. It was a simple plan.
Kill all humans.
Skippy had seen the future. He had been to the past. He vacationed in the present. When an undergrad at MAD's School of Science, he had built a device that allowed him to monitor alternate timelines; it was then he decided upon his true role in this world. He would allow the planet to develop as it should have.
Humanity, he had been shocked to learn, was a failed experiment. The planet, amazingly subtle and remarkably intelligent, wanted to see how well an advanced primate would fare if given intelligence. The answer was "not very well," as the new species was inherently bent towards war and destruction. Within a short amount of time, three promising species were wiped out. Resources, therefore, would go towards an advanced dinosaur species, who were given subtle instructions to destroy the primates.
The arrival of Lavos, however, changed everything. It slammed into the planet with such force that it had to pull all its resources inward just to heal itself. The surface was plunged into an ice age and the dinosaurs were wiped out. The primates, however, survived due in no small part to Lavos' interference.
Lavos' emergence in 1999 was caused by contact to its shell by a mining consortium, mistaking the outer shell for an ore deposit. The pain caused by the removal of a significant portion of one of its spines caused Lavos to defend itself in the only way its species knew how.
It destroyed the surface of the planet.
However, small groups of humans survived. In their desperate attempts to survive, they accidentally triggered ancient stockpiles of weapons. The seas became a toxic purple sludge. The land was burned, unable to support plants. The skies darkened in a perpetual electrical storm.
Skippy used the knowledge he gained during his graduate student years to learn how to build a device that could pull objects from the Tesseract, the void beyond the realm of existence. He researched how to increase the power output of a Lavoid's defensive attack. Most importantly, he calculated how much extra power Lavos would have needed to completely destroy all life on the surface of the planet, eradicating humanity and giving the planet a clean slate.
His PhD program years were spent building a device that could pull Lavos from the Tesseract. Naturally, he told his peers and professors that he was designing a new reactor for faster-than-light space travel. It did, in fact, work along the same principles.
Ironically, his design WAS able to propel a manned spacecraft beyond the speed of light. Unfortunately, all contact was lost with the crew when they flew directly into Theta Centauri, the nearest star. A second attempt met with another poor end when, unbeknownst to them, the governor on the engine was disabled and they accelerated far too quickly, turning the crew into a one molecule thick film on the rear bulkhead of the cockpit.
And so, from his lab in 1488 A.D., he was finishing the device that would successfully pull Lavos from the Tesseract and return him to his rightful place in history. Only this time, his destructive output would be increased a thousand fold. And in doing so, Lavos would destroy himself.
Humanity would be destroyed. Lavos would be destroyed. And the planet would be allowed to heal.