Crono was killed rescuing the rest of the party (and Schala, Magus, and Queen Zeal) from Lavos in the Ocean Palace. Magus told you to talk to Gaspar to possibly get Crono back, so talk to him. If that doesn't help, talk to Belthasar, the Guru of Reason. If you can't find Belthasar, note that the four time-warped Zealians each landed in a different era. Janus was sent to the Middle Ages, Melchior to Crono's present, Gaspar to the End of Time, and Belthasar to the Future; specifically, the Keeper's Dome, where you encountered him (well, a Nu with his memories) when you got the Epoch. If you still don't know what to do, it's time to consult a guide; there's enough information given to piece things together (by old RPG standards) but it relies on you remembering the Zeal arc. As for the mutant in the Black Omen, a bunch of sidequests have opened up now that you have a flying time machine. Those sidequests will give you more than enough levels and gear to deal with that mutant. The easiest ones are the Northern Ruins north of Choras and the Sunken Desert (may not appear) near Fiona's house in 600 AD.
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