Ok, I finally figured it out!
We all know Lavos is responsibile for the Gates, and we know the Entity was guiding Crono! Reading the boards, I found out that the Entity was responsible for all sorts of things in Chrono Trigger, right? What if that was Lavos, too? He did try and kill Marle by senting her to the DBT!
So you're wondering, but isn't Lavos evil? Why would he try and let Crono kill himself? Because he had a Multiple Personality Disorder! Lavos' Core was made of three parts, each with a seperate personality! We have the middle part, Lavos as we know him, the Right Bit who THINKS he's Lavos, so when you kill him he blows up his brothers, and the left Bit, who's the good side and the reincarnation of Schala (How else did she merge with Lavos?)
Also note that at the end, Lucca said the Entity was finally at rest, and Lavos is DEAD! Also, when you beat Lavos, you see the shadow of the left bit, Schala. That's how she gets sent to the DBT at the end! You know it's true! It's the best theory EVER!
"Hi, I'm newbie Ned. I'll be over there sucking a shotgun. Don't touch the sides!" *BLAMMO!*
