To get this ending you will need to fight lavos right after you get the epoch back from Dalton. After this you will need to go to the north Cape to meet Magus. At this point I let him live although you can choose to kill him if you want. After Magus you will see the Ocean Palace rise from the sea to become the Black Omen. At this point I returned back to the end of time to obtain the chrono trigger from the guru of time. Next get into your ship and warp to 1999 AD and command the party to ram Lavos with the time machine. This will effectively put you on the path to the second version of the reunion ending.
In this ending everyone arrives at the end of time after defeating lavos and it begins to play out the same way as Reunion version 1. However after you warp back to the fairgrounds everyone else in your party will be scattered around the fairground. Each time you talk to one of them they will jump toward the time gate at the north end of the fairgrounds. Once you speak to everyone go to the time gate and the rest of the ending plays out with marle taking a balloon ride at the end.