Here's the deal. I haven't played or thought about this game in like a decade, so if my places/names are off, fuck you:
It's many years later. Chrono and Marle have married, Lucia has also married some handsome Librarian/academic type. They have kids who run around on adventures. These kids amount to Chrono, Marle and Lucia. Scampering around the forest one day, these kids find the site of the old Millenium Fair, including a partially functional time machine. The kids zap to a Lavos-free future which is still post-Apocalyptic. They fight through a junkyard, whatever, they get cornered by the BIG BADDIE. Just when all looks lost, the big baddie muscle-y Post Apocalypse guy gets taken out by a bunch of dude in cloaks.
to
The dudes in cloaks reveal themselves to be The Follower of Lavos. They look to resurrect Lavos and prevent the fall of that floating city of which THEY ARE THE SURVIVORS. They corner the kids, ready to kill them when WHAMMO. Out of nowhere. What the fuck! It's Magus and Frog! They've put aside their differences, uniting for great justice! It seems that all of the Chrono crew's time hopping caused any number of time discrepancies, which Magus and Frog use the Epoch to fix. When the player boards the Epoch, OH FUCK WHO IS DRIVING! It's Gatto! Magus, Frog, Gatto and the kids barely escape the Follower of Lavos, the whole crew returns to "Present Day" and reunite to discover who the Followers of Lavos are, what they want and how to stop them.
Was that so fucking hard?