The Master Program is the true last boss from Battle Circuit.
He is the entity which controls the Shiva System, materialized after the system is activated by Pluto. As the five bounty hunters defeat Pluto, the Shiva System materializes him, so he unleashes his power, freezing Dr. Saturn and taking the entire ruins up to the sky. The bounty hunters challenge the Program, so he initializes his defense program, Program Genocide, to exterminate everyone.
After a fierce battle, the bounty hunters defeat the Master Program, taking Dr. Saturn with them and escaping, while the ruins explode.