Serge is a young boy from a fishermen's village. One day, while strolling on the sea shore with his sweetheart, Serge suddenly disappears. He comes back to senses several moments later. Everything seems just the same as it was before, but when Serge visits his home village, nobody recognizes him. He hears from people that he has been dead for ten years. Serge begins to realize that he is now in a parallel world. His first and only wish is to find a way to return home, but, in order to do that, he must understand what has caused the existence of parallel words, allowing inter-dimensional travel. His quest will also reveal to him the truth about his own existence.

Chrono Cross is a Japanese-style role-playing game, and a sequel to Chrono Trigger. The game's story is not directly connected to that of its predecessor, though there are sub-plots and characters that refer to it. Combat in the game is turn-based; like Chrono Trigger, the game has no random battles, and enemies are always visible on screen. During battles, Serge and his party members can perform three kinds of attacks: weak, medium, and strong, which tend to miss more frequently but inflict more damage. Actions in battle deplete a certain amount of stamina, which recovers as other characters act. There are also no character levels in the game: instead, the characters get their parameters increased directly after each battle.

All magic spells, character-specific tech attacks, and consumable items are grouped into six elements, which are divided into three pairs with opposing properties. Each player-controlled character and enemy has an innate element, which enhances the power of spells categorized under it when used by said character, but also weakens his or her resistance to the opposing element. Battle fields may also be marked by a particular element, granting bonuses to attacks based on it, and reducing the damage caused by the opposing one. Player-controlled characters have differently shaped grids which allow the player to allocate purchased or found elements there. When the character participates in a battle, the allocated elements act as equipped spells, and can be cast until their amount is depleted.

Though most of the plot progression is linear, there are several sub-quests that are not required to complete in order to reach the game's ending. The game features many recruitable characters (up to 45, though not all of them can be recruited in one playthrough), several different endings, and the ability to play the game again with the statistics and items from the previous play.