Notwithstanding this the English tried to rope him in anyway as the most powerful man in Ulster. But Shane was determined to keep his distance and be his own man as much as he could. After engaging in conflict with the Earl of Sussex and managing to evade his enemy’s traps he was granted safe passage to London. In 1562, accompanied by the Irish Earls of Ormonde and Kildare, he had an audience at the Court of Queen Elizabeth I. Her courtiers were agog at Shane’s Bodyguard of Gallowglass warriors and his own apparel. The Queen however did not want an expensive War against this colourful Gaelic Chieftain and cut a deal with him. In return for recognising her position as Queen she would recognise him as the O’Neill and both sides agreed to a more pacific relationship in future.
On return Shane quickly suppressed any dissent within his own lands and then waged War against the O’Donnell’s of Donegal and the MacDonnell’s of Antrim. He raided into Fermanagh and used his new found legitimacy to shove his weight around. But these attacks proved disconcerting to the English who did not want Shane, or any other Gaelic Leader, to gain sway over the other Chieftain’s and prove a thorn in their side. Divide et impera was the name of the game as far as the English were concerned - and Shane was not playing it their way. Elizabeth at last authorized Sussex to take the field against Shane, but two separate expeditions failed to accomplish anything except some depredations in O'Neill's country. In 1565 O’Neill defeated the MacDonnell’s at the Battle of Glenshesk and took Sorley Boy MacDonnell prisoner. He also held as his captive one Calvagh O’Donnell, who he allegedly kept in cage while he took his wife for his mistress! O’Neill also armed the common people to fight his wars and hired bands of Scottish mercenaries to augment his forces. By this stage he was the most powerful man in the North and for the moment the English had to recognise like it or not.
By 1566 they had had enough though and an expedition was dispatched to Derry to establish a fort there. Meanwhile Lord Deputy Sidney marched from Dublin with a small but well armed force, which traversed the O’Neills heartland in Tyrone, pillaging and burning and turning the lesser Chieftains against him. The following year Shane decided to strike back and re establish his sway over the O’Donnell’s of Donegal.
But in May 1567 he suffered a shock defeat at Farsetmore at the hands of these O’Donnell’s. He had to flee the field of battle with just a small band of followers. While still feared he had no true allies and in desperation he threw himself upon the mercy of the MacDonnells of Antrim of all people. It is not certain whether his death was a deliberate act of assassination or the result of a fracas but his demise was greeted with relief in Dublin. The balance of probability is that English agents bribed Alexander Og MacDonnell, his reluctant host, to kill him. The English demanded his head as proof of his death. On receipt it was dispatched to the City where it was displayed upon the walls of Dublin Castle. Thus ended the violent and bloody career of one of the most formidable and colourful characters that 16th Century Ireland produced.