Because it was unlikely that a jury in County Armagh, where many people remained frightened of the O'Neills, would convict him it was decided to try him in Dublin instead.
Despite attempts by his powerful and influential uncle Hugh O'Neill, Earl of Tyrone to have him pardoned the sentence was still set to be carried out.
[1] The steadfast refusal of the Viceroy of Ireland Sir Arthur Chichester to overturn the death sentence, convinced Tyrone that his power was being weakened despite his generally good relations with James I in London.
This was a factor in his decision to take part in the Flight of the Earls which took him into exile in Italy.
[2] The Earl's departure sealed the fate of Brian who was hanged on the reduced charge of manslaughter.