Zeal was significantly draining his power through the Mammon Machine; when the device was moved to the bottom of the ocean floor, the leeching was sufficient to cause concern for Lavos, who obliterated the perpetrators. In 1999 A.D., human civilization was probably nearing a level of technology that could possibly challenge Lavos. Also, it is probably that a few hundred years down the road, Chronopolis might come to pass (or another temporal research facility that could strike Lavos with a time-based strategy). Lavos destroyed humanity at this moment in order to prevent any possible threats. However, unlike the case in Zeal, where Lavos only had to destroy a floating country, here Lavos exploded the entire surface of the planet to completely render civilization derelict. This also allowed the planet to serve as his spawning grounds without interruption; he subsequently reproduced asexually at Death Peak, where the spawns roamed. Eventually, after absorbing a certain amount of power, they were to leave the planet and seek out other targets in the galaxy. This process was interrupted when history was changed so that they never existed.
However, the above reason for 1999 A.D. does assume that Lavos was somehow able to sense technological advancement, implying a very conscious act. Odd Water offers a different explanation:
This line of action (Lavos sensing a threat in 1999 A.D.) suggests a far greater line of reasoning and intelligence, which would lead to Lavos being along the notion of 'evil' and not just living out a life-cycle of survival. If Lavos could judge the future high-tech world as being a threat, there is no reason why it would not have been able to do the same with Zeal when they first started to drain energy from Lavos.
My theory for the Day of Destruction is this; that the eruption upon 1999 A.D. was just a natural point in the life-cycle of the Lavos species. Lavos was already on the planet for a very long time absorbing energy and DNA from species. My suggestion is that by 1999 A.D that Lavos already got enough DNA from creatures and thus needed them no longer. So it erupted to the surface and rained down its destruction from the heavens to clear off most or all of the surface life. Thus giving its spawn a safe place to be deposited for them to grow mostly undisturbed. This would then last until the spawn are large enough and stored enough energy for their own trips out into space, as per the exploding the planet theory of mine before covered.
From: Common Questions