Someone wrote a "sequel" of sorts to Chrono Trigger back in my AOL days on ANTagonist, Inc where humanity had achieved interstellar spaceflight, and taking down Lavos Spawn was a somewhat common occurrence. Like, Lavos, as powerful as it is, is still an organism. It didn't come from nowhere. It was birthed by another Lavos-like entity and sent to Earth. So as the human empire expanded, getting a Really Big Gun on their spaceships to kill any planetary parasitic Lavos-like organisms was a must.
I can't remember the rest of the plot, sadly. I think what happened is that one of the Lavos-like organisms used its power to alter time, and the Chrono Trigger heroes had to go and stop *that* Lavos organism from doing something to stop humanity from existing--without creating a paradox? Maybe.
The fanfic was before Chrono Cross came out in the US for sure.
Oh yeah. In the Chrono Cross universe where Chronopolis existed (not Dinopolis), I kinda always wondered why *they* didn't have a plan before Dream Lavos or whatever made a plan to come back somehow. Like, I don't get Chrono Cross. No one understands Chrono Cross. Xenogears? 8th grade reading material. But to understand Chrono Cross you gotta have like your Doctorate in Anime. But anyway, it seemed Chronopolis "existed" in the future and was doing stuff with FATE "before" the Lavos you fight at the end of Chrono Cross "existed" and Chronopolis should have predicted it. They could have built a Time Nuke to kill that Lavos off, for sure.
Anyway, to answer the question: Lavos is so powerful that it exists beyond the flow of what we see as linear time. You would need, like, a super special TIme Nuke already planned for its emergence, or a time machine *and* a nuke of specific proportions to take it out. I think the final final battle in Chrono Trigger, where you're fighting the Lavos cores, exists in a "special" sort of time that makes Lavos' death "mostly" final. Like. I'm not even sure what I'm talking about anymore, but its temporal field could, like...if the Lavos of 1999 AD were destroyed by regular nuclear weapon, the Lavos of 1000 AD (or 1998 AD) would still be alive, and would "know" what the future held for it, and adjust the timeline accordingly. It's a three man team that has to get inside and do the job is Weird Temporal Dimension Stuff.
I'm gonna nap. I'm not sure I had a point. Sorry