Once Lavos is defeated and sent to the Darkness Beyond Time, it finds and merges with Schala, creating the being that will eventually become the Time Devourer and will, if unchecked, destroy all of space-time.
It's my belief that once this merging happens, an Entity becomes aware of the threat and seeks to empower Crono with the ability to defeat it by leading him to the Dimensional Vortices. This Entity may be the spirit of the planet, reprising the role it played in creating the Time Gates, but I suspect it is actually a different Entity: the spirit of existence itself, since the stakes are much higher than the life of one world. Obviously this plan doesn't work, else we wouldn't have the events of Chrono Cross, but it was certainly worth a shot.
I don't have anything to back up this theory; it's just supposition on my part. And I have an even shakier tangential theory concerning the Lost Sanctum.
I propose that with the barriers between dimensions becoming thin due to the introduction of the Vortices, the Planet-Entity of the Reptite timeline reached across the worlds and created the gates to the Lost Sanctum in an attempt to save the Reptites of Crono's dimension from extinction.* Not as some kind of scheme to return them to prominence and take revenge on the humans, but as a simple maternal desire to see her "lost children" survive.
Again, just idle supposition with nothing to back it up. Indeed, the fact that the Lost Sanctum gates appear before the Dimensional Vortices on the first play-through would seem to refute it. I don't have an answer for that other than an unsatisfactory, "Hey, time travel."
* To go on a tangent of a tangent and further refute my own theory, I'm not certain the Reptites went completely extinct in the human timeline (not counting Chrono Cross's Dragonians which are known to have died out). The reason being the presence of the Green Ambler at the Millenial Fair. However, since nothing is known of this character beyond a love of racing, we can't say for sure whether he is an actual Reptite or just some sort of Mystic or demi-human who reuses the Reptite sprite. But the non-canonical "fact" that the Ambler is replaced by a human in the Dino Age ending would seem to imply that he is indeed a surviving Reptite. (I'm basing my assumption of the Ambler's gender on the fact that its Dino Age replacement is a male sprite... That's a lot of assumptions!)
