Aonghas became a rebel against both his father and the Scottish crown, in a civil clan war which would see the end of the independent Lordship of the Isles.
In 1476, a secret treaty that was made by Aonghas's father, John MacDonald, with King Edward IV of England was discovered by King James III of Scotland, who then stripped MacDonald of his earldom, as well as the sheriffdoms of Nairn and Inverness, and the lordships of Kintyre and Knapdale; the King however confirmed MacDonald with the remainder of his lands and the title Lord of the Isles.
Aonghas gathered his forces and those of his allies against the armies of his father, and a great sea battle took place near Tobermory, the Battle of the Bloody Bay, probably in the year 1481, in which Aonghas defeated the galleys of his father's west highland allies.
In the same year, another battle took place at Lagabraad, in which Aonghas defeated a royal army led by the Earl of Atholl.
The murderer was his harpist, Diarmaid O'Cairbre, who carried out the act for reasons which remain unclear.