With Dalton's massive flying machine in the ocean and your path ahead clear - that is, looking for a way to bring back Crono - head to the Last Village. Talk to the villagers and one will mention a suspicious figure at the North Cape. Put Frog in your party for extra storyline content and head there.
Once there you'll find Magus, a fellow survivor of the Ocean Palace debacle, who reveals the extent of his history with the era and Lavos. He then insults Crono, goading Frog into a fight - and if you want, you can take the sorcerer on again, mano a mano, with the amphibian swordsman. Beating Magus frees Frog from the curse at the end of the game but kills Magus, whereas declining the fight earns you Magus for your team. The second route is much more beneficial for your team, though to experience the entirety of the game you may as well kill Magus at least once. In either case Magus reveals that Gaspar, the Guru of Time, may know how to bring Crono back.
Head to the End of Time with your now-flying Epoch and talk to the old man. He'll offer his condolences for your loss. Proceed to leave once he stops talking and he'll call you back. Return and he'll offer you the Time Egg, which has the potential to bring Crono back. You must fulfil two criteria for it to work, however.
The first is getting a Crono clone, and doing so requires you to head to 1000 AD's Millenial Fair. Head to Norstein Bekler's tent and he'll offer you a challenge: complete his matching game and you'll get a clone. Use the buttons he indicates in-game and match the clone's expressions as best you can. The better you match them, the less expensive the clone will be, to the point that you'll get it for free. If you're short on silver points for his challenge, go wail on Lucca's Gato robot for a while. Go to Crono's house for the clone.
Head to 2300 AD next, returning to Epoch's home base. Once there Belthasar's Nu body will release a series of dolls to the nearby Death Peak, allowing you to complete the next step: head to the summit of the peak.
This can prove tricky given the mountain's geography. Your first task is to scale the base, walking when the wind has abated and hiding behind trees when it's picking up. The only other tricky part of the mountain is an icy path that you should run across quickly, staying close to the middle to avoid falling.
The mountain's enemies aren't terribly strong, though you'll want magic to get through easily. Magus or Lucca will tear up most of them with Fire II. The three Lavos Spawn you're forced to face are another matter, however, as an all-hitting spell will push them to retaliate with needle attacks. Bring a strong single hitter like Ayla or Robo to attack their heads and you'll kill them quickly. Make use of any save points you find as they're always a sign of impending trouble.
Once you beat the last spawn you'll notice its shell doesn't dissolve. One of the Nu's dolls will offer a clue to its purpose: push the shell to a nearby series of handholds and climb to the peak. Once you do so a long cut scene will start, and once it's done Crono will be back on your team.
At this point you are free to do as you wish. You can challenge Lavos right away and end the game; however there are tons of side quests to be completed as well, and since Lavos is still probably too strong for your party it's well worth embarking on these quests to gain new power and items.