If you're going to look at my "Entity" theory (really, it's a theory on how in-game evidence points to a conclusion that the Gurus were more involved in the events of Chrono Trigger than we see directly, and that they could have influenced the events of Chrono Trigger to a significant degree), definitely put aside a good amount of time - just about the whole thread is a good read.
To see what's pretty much the completion of my theory (may need a few adjustments - we'll see), go here:
http://www.chronocompendium.com/Forums/viewtopic.php?t=1958&postdays=0&postorder=asc&start=63