You get this ending by fighting lavos after Crono gets destroyed by lavos in the “New game plus” mode. Basically after you challenge lavos and loose, on purpose this time, you are forced to fight through the blackbird and defeat Dalton. The ocean palace becomes the black omen and you get the epoch which now has wings. At this point I went north to defeat magus on the cliff so that Frog could change back into Glenn for the ending, although this is not necessary for the ending. The next thing to do is warp to Gaspar to get the Chrono trigger egg and then go after lavos without crashing the epoch into him.
In this ending everyone appears at the end of time and Gasper reveals that the time gates will close. Everyone is in a panic and rushes back to their own times leaving Marle and Lucca begging for them to save Crono. Eventually they reappear at Lucca’s telepod on the fairgrounds and everyone is now in a search for Crono. You follow suite in the Epoch and the ending proceeds the same as the Beyond time ending.