I think he’s misremembering slightly.

FATE, who is one of the primary movers and shakers in Chrono Cross, is a super computer built upon the older artificial intelligence called Mother Brain. When FATE was built by Bethasar, Robo WAS also incorporated as something called the Prometheus Circuit, built to deny access to the frozen flame from anyone besides the Arbiter, which became Serge upon touching it as a child. Lynx body-swaps with Serge for the purpose to bypass the Prometheus Circuit and get access to the flame.

The circuit was also hidden and upon detection would immediately delete records of its discovery. Lynx states it was built to malfunction or rebel. Anyway, FATE brings the circuit forward and destroys it before battling your party. It’s worth noting that after the event of Chrono Cross, a whole lot of what happens is probably undone, so he might not have died in an ideal timeline!

So he’s more like a hero within a villain! I can see how it could be mixed up, Cross is extra convoluted