The Commission is an organisation overseeing, and managing the space-time continuum. Their main job is to make sure that all events that are supposed to happen, happen. To do this, they have agents ready to travel through time and to eliminate anyone that poses a threat to their job. Agents are assigned their tasks by the management of the Commission. Tasks are given to the agents with the help of pneumatic tubes. Their residence is the year 1955. For a brief period of time, Five is employed by the Commission.
It is implied that the Handler is just a small cog in the grand scheme of the Commission and could be easily replaced. She tells Five this during the scene where Hazel and Cha-Cha are going to contact the Commission in return for the Briefcase. This implies that she could be easily replaced and that there are higher beings above her in the hierarchy.