Finally returning to Another World and teaming up with the formerly antagonistic Acacia Dragoons to rescue Riddel from the Porre Army. Afterwards Riddel, General Viper, Fargo, Karsh or Zoah and Marcy all join your party to hunt down the traitorous Lynx. You literally have several previous antagonists become playable characters.
The final showdown with Lynx/FATE. For most of the game Serge has been constantly one step behind Lynx in his attempts to gain access to The Frozen Flame, even spending half the game trapped in Lynx's body and losing all his previous party members including his Implied Love Interest Kid. To say that finally catching up to and beating the manipulative Lynx is satisfying is an understatement. Especially since he has spent most of the game as the Big Bad and the Arch-Nemesis of both Kid and Serge.
The "Save Marbule" sidequest also known as the Magical Dreamers Sidequest. Initiated during Serge/Lynx's visit to the S.S. Zelbess in Home World it sees Nikki and his band Magical Dreamers agree to perform a sacred Demi-Human song in order to save the town of Marbule though they must first convince the captain of the S.S. Zelbess (and Nikki's father) Fargo. Bringing Another World's Fargo to meet his Home World counterpart causes him to admonish the other Fargo and forcibly sail the Zelbess to Marbule himself. Nikki and the Dreamers then give the concert of a lifetime as Marbule's Theme the Sage of Marbule taught Nikki is rearranged into the epic Magical Dreamers ~Wind, Sea, and Stars~. Fargo then unlocks his ultimate Level 7 Tech Invincible and the main party is able to clear out the monsters from Marbule saving the town. Doing so also unlocks the battle with the Black Dragon in Another World where Fargo can steal the extremely useful Black Plate Armor.
Discovering the Frozen Flame in Chronopolis and speaking with The Prometheus Circuit (aka Robo) is pretty memorable, too — not "awesome" as in "cool", per se, but the imagery, music, and information being conveyed to you at that moment are all pretty awe-inspiring. If only he stuck around longer.
When you finally get Serge's body back. After having to go back and forth between Another World and Home World to both gain the Dragon Relics and reforge the Dragon's Tear the pay-off is worth it. Especially since by getting his body back means Serge can finally enter The Sea of Eden and catch up to Dark Serge/Lynx and put a stop to him.
Successfully casting the Chrono Cross Element in the final battle with the Time Devourer.
"I have been waiting an eternity...just for this very moment..." And Schala's soul is freed and healed, and Lavos finally melts away. It may have been Guide Dang It!, but that is how one defeats a god.
