Who manipulated who in Chrono Cross?
Chrono Cross features many cases of manipulation and transcendent control. Starting at the bottom, Wazuki was controlled by the FATE supercomputer and made to do its bidding as Lynx. Erstwhile, FATE had been duped by the Prometheus Circuit; the supercomputer had no idea that the circuit even existed before it engaged and locked the Frozen Flame's access. Expanding the scope, FATE manipulated the people of El Nido through the Records of FATE. Through Lynx, FATE manipulated Serge into switching bodies at Fort Dragonia. Later, Lynx manipulated Kid after the Fort Dragonian incident. Switching to the other side, the Time Devourer consumed the Dragon God, probably manipulating it afterwards. Consider that the Dragon God stole away the Frozen Flame, which Serge needed to defeat the Time Devourer; it served it in this manner. Harle reported to the Dragon God, and in the end had to fulfill its wishes rather than stay with Serge, who she had come to love. The Dragon God itself manipulated Serge by convincing him to destroy FATE, which allowed the Dragon God to take the Frozen Flame. Before this occurred, Harle had manipulated Lynx for some time as she traveled with him to gain his trust and get closer to the FATE supercomputer.
By far, the man in charge is Belthasar, who planned all the events in the game and knew the outcome beforehand. He ultimately controlled everyone until the final battle, when Serge consciously decided to face the Time Devourer and free Schala on his own merit.
From: Common Questions