This ending is achieved through the new game plus mode and can be accessed after defeating Azala. It will remain available up to the point where you view Schala opening up the sealed door with the amulet. Basically once you get to the Dark Ages 12000 B.C. start looking for a way to gate to Lavos.
The ending sequence consists of two sets of scenes shown simultaneously. One is your party members doing various activities and the other is Magus going after Lavos on his own. It concludes with Magus infiltrating the Ocean Palace and entering the final room to confront Lavos and presumably the Mammon machine.