Musa held the imamate through the height of Abbasid power, under rulers whose claim to authority rested on descent from the Prophet's family and who therefore treated a rival claimant within that family as a direct threat. His response was quietist. He made no bid for power, taught within a restricted circle, and made extensive use of the principle that a believer under threat may conceal his position.
The institutional development attributed to his period is the network of agents. Representatives in Kufa, Baghdad, Egypt and the Iranian provinces collected the religious levy from followers, transmitted questions and rulings, and maintained contact with an imam who was frequently under surveillance or in custody. That arrangement outlasted him and became the framework through which the community was administered during the later imamates and, after them, during the concealment of the twelfth imam. A community that could function without direct access to its leader had to build the means, and this is where the means were built.
He was arrested more than once and died in 799 in Baghdad while held by the authorities. The tradition holds that he was poisoned; the reports name officials and vary in detail, and no version is independently confirmed.
He was buried in a cemetery north of Baghdad which grew into the town and shrine of Kadhimiya, where his grandson Muhammad al-Jawad, the ninth imam, is buried beside him. Successive dynasties rebuilt and enlarged the complex, and it remains one of the principal places of Shia pilgrimage, standing inside what is now the city of Baghdad itself.