In order to ensure his continued existence within the Brotherhood, Hassan cut a deal with General Solomon - in return for intel on Nod activities, GDI would allow him to lead the Brotherhood.
Hassan is a weak ruler, keeping the Brotherhood away from total oblivion by the tiniest of hairs. He also acts as GDI's cleaner, removing the more dangerous elements of Nod, typically by killing them.
Cover it up and kill [Slavik] before the truth comes out... and Hassan, if he gains more power, you will become useless to us, and useless things have a way of disappearing. - James Solomon(src)
Acting on orders from Solomon, Hassan had the Black Hand prelate Anton Slavik arrested on trumped charges of GDI espionage. He sentenced the Serbian commander to death, but before the sentence could be carried out, Slavik was sprung by Oxanna Kristos and Slavik's loyalists, setting in motion events that would end with Hassan dead. In hindsight, Hassan realized attempting to eliminate Slavik in such a manner was a big mistake and his adversary had more support than initially thought, so he tried to beg Solomon for help, but all he got in return was a cold shoulder.
Hassan used mass media to maintain control over the Brotherhood. Slavik struck a critical blow to the regime by capturing and subverting the mass media outlet responsible for much of Hassan's propaganda. With many of his followers deserting him, Hassan was eventually besieged in a Pyramid near Cairo. Hassan attempted to escape in a Harpy as the defenses collapsed but was shot down and captured.
Hassan was personally executed by Slavik at a Nod rally. The execution also marked the public return of Kane.