Just on brief reflection of the storyline, since it opened gates to collect the heroes from different timelines, Lavos would prevail, having maximum 3 heroes to take it on in any one timeline; (Crono, Lucca, Marle). However, they would be unprepared, unleveled, and unknowing of the impending doom. I would assume it would carry out as the timeline begins, where lavos consumes the planet, and attacks, destroying everything and leaving it as shown in 2300AD.