Dalton went to the Darkness Beyond Time. There he used Schala to somehow exit it with Lavos. They formed a space station/doomsday device as Lavos had used the majority of his power to channel through Schala's pendant and escape. Blah blah sideuest etc. side-villain blah blah. Than Lucca changes the Epoch for space-travel and they reach the Astro Dalton Imperial (couldn't resist). Big dungeon, then you face Dalton. Than you see many little outlines of the true Lavos come around Dalton and then he turns into the....
Name: Dalton-Lavos Omega
Stats: No clue
Element: Shadow
You face a him, and then Lavos reguritates Dalton *snicker* and begins to operate the machine. You make an attempt to hurt him, but he doesn't even seem to notice. Dalton has a change of heart (big surprise) and says the only way to stop Lavos is through the self-destruct button. However, it is so far away from the docking bay, the presser wouldn't be able to escape. Magus offers to go (or someone else, depending on your party), but Dalton goes. You escape in a Metroid like fassion.
Here's something else, the side-villain, much like Magus in CT, appears to be the main villain. This idea is more suitable for fanfiction but hey. The side-villain is Mother Brain. Not RY Mother Brain, but sit-in-a-glass-vial-getting-beaten-extremely-easily-while-my-plan-to-replicate-the-Metroids-has-failed-Mother-Brain. Samus comes into the picture from the new future. She thinks your evil, you face her, blah blah, and she joins you. She has powerful shadow magic. And I assure you she's Schala involved, of course.
Viola. Chrono Break.
Then, after the ending, and even the THE END, you see a dark outline of Schala. Then a Lavos outline appears, then Schala seems to disintigrate. Then he morphs into the Time Devourer. Then you see Schala on top, then she makes one of Magus' trademark evil smile.
This is the truth. This is my belief. At least for now.