The purpose of a MUTO Prime is to infect other Titans with parasitic eggs, which will feed off of the Titan host and kill it before birthing MUTOs, who will proceed to breed rapidly and destroy the global ecosystem. If the MUTO Prime dies or more than one is needed, any female MUTO can eventually metamorphose into one. Dr. Emma Russell theorizes this is done by the female MUTO consuming a male, similar to Mantises.
This individual MUTO Prime was first seen by ancient humans battling Dagon, a member of the Titanus Gojira species. After beating Dagon to the brink of death, the MUTO Prime proceeded to inject him with her parasitic eggs. The eggs fed off of Dagon's blood, which eventually killed him, before hatching the male and female MUTOs seen in 2014.
After the death of her offspring at the hands of Godzilla, MUTO Prime awoke once more to jump-start the MUTO species by hunting Godzilla. Over the course of several battles, MUTO Prime gradually weakened Godzilla. During their final confrontation, MUTO Prime was killed by Godzilla after the latter crushed her head with a powerful stomp.