The Master of Synapse reigns as the supreme ruler of the floating realm above Earth. This entity created the Angeloids, artificial beings designed to serve masters from Synapse or humans on Earth within a strict hierarchy demanding absolute obedience. Viewing humanity as chaotic and destructive, the Master pursued their elimination, initiating conflicts that escalated into assaults on Earth.

The Master's motivation centered on erasing human existence, perceiving their chaotic nature as a threat to cosmic order. This character orchestrated the Angeloids' deployment, including strategic battle-class units like Ikaros, originally designated as the Uranus Queen who destroyed the Tower of Babel during an earlier descent. The Master's authority remained unchallenged until the final arc, prompting direct intervention.

A critical turning point occurred when the Master attempted to absorb the core of Chaos, a unique self-evolving Angeloid. This act triggered instability within Synapse. During the ensuing confrontation at the realm's core, a human wielding the power of Ikaros' core—after her sacrifice—defeated the Master. The battle concluded with the Master's physical form disintegrating, ending their rule.

Following the overthrow, governance of Synapse transitioned to Daedalus, who initiated reforms focused on peaceful coexistence with humanity. The Master's legacy persisted through the Angeloid system and Synapse's societal structures, now redefined under new leadership. The character was never resurrected or returned in any sequel media.