Spanish Armada and renewed rebellion
In September 1588, upon news of the flight of the Spanish Armada into the North Sea, Bingham ordered that all Spanish refugees landing on the coast of Connacht should be brought to Galway and put to death there. Many vessels were wrecked in the following month, and of the survivors who came to shore he estimated that 1,000 were put to death under his authority. His brother George, sheriff of County Sligo, also killed many Spanish survivors. Bingham suggested that 50 of the captives be kept alive, but the new Lord Deputy of Ireland, William Fitzwilliam, ordered him to put them all to death; later, more survivors came into his custody and he put them under the charge of bailsmen. (Some years later, in January 1592, Bingham persuaded several Spaniards to come in from the Burkes under protection and sent them to Dublin for passage home, but they were detained in prison there against his wishes.)
In September, Bingham marched out with a small force toward the castles of Doona and Torrane, on intelligence that hundreds of survivors under the command of Don Alonso de Leyva had left those strongholds and marched to Donamona to intercept another landing of 500 men. Punishment was meted out to those suspected of succouring the Spanish. By the end of September, few Irish lords refused to give up their Armada survivors, but the presence of the Spanish caused unrest among several clans. In March 1589 open rebellion was entered by the pretender to the title of the MacWilliam – the Blind Abbot of the Burkes – and by other western clans. Fitzwilliam intervened and laid waste to counties Mayo, Sligo and parts of Roscommon, ordering Bingham to withdraw his forces from Mayo so as not to hinder the pacification.
A peace commission was set up, with Bingham at its head, which sat in Galway in April, but most of the rebels stayed out. Then Sir Brian O'Rourke committed a great cattle raid in County Sligo, while the Burkes took similar action in the southwest, across the Mayo border. The latest rebel demand was for the withdrawal of Bingham from Connacht, the installation of the MacWilliam, and the removal of sheriffs from Mayo. Chaos reigned in the province, while the authorities remained divided on how best to proceed. One faction in the Privy Council of Ireland put the collapse of the talks down to the desire of some of the peace commissioners to blame Bingham for the rebellions.
Bingham pursued his policy in the field, scouring counties Mayo and Roscommon with his forces, until the rebels had caved in and O'Rourke was driven north into Ulster. At Cong he was ordered by Fitzwilliam to cease and to disband some of his newly raised forces, and a new peace commission was appointed to treat until Fitzwilliam arrived. The Lord Deputy was determined that blame be placed on Bingham, and the rebels were resurgent as Fitzwilliam ordered the governor to remain at Athlone. Fitzwilliam travelled to Galway with 350 foot and 120 horse to receive the formal submissions of the rebels, and two books of complaints were lodged by them against Bingham. The complaints were forwarded by the lord deputy into England, and before leaving the province he denied Bingham the use of martial law and cut off his authority to conduct assize sessions, until Fitzwilliam himself had completed his progress through the province.
Connacht remained unstable, and O'Rourke broke into action again, attacking the sheriff of Sligo in the Curlew Mountains. Trouble spread across the north, despite the presence of the lord deputy, and the disablement of the governor became a strategic worry for the government in London. Walsingham wrote in support of Bingham, and the Privy Council at London ordered that a trial before the lord deputy and council at Dublin proceed on the basis of the books of complaint. Fitzwilliam set about gathering evidence against Bingham, but crucial testimony from absent rebels was lacking.
In early October, the Blind Abbott was proclaimed MacWilliam, and the queen ordered Fitzwilliam to assist Bingham in suppressing the title. But support from England could not prevent the charges against Bingham from being read before the council in early November. No witnesses appeared against him (although there were mutterings that they were too fearful to come to Dublin); his own witnesses underwent examination on the 28th. His full acquittal was proclaimed on 5 December.
Bingham returned to Connacht, where the Lord Deputy had gathered his forces at Galway with an invitation to the rebels to submit by 12 January 1590. Hardly any rebels of note accepted, fearing that their hostages would be inadequate and that they themselves would be detained. Bingham was then given a free hand, and promptly marched to Cong with Donogh O'Brien, 4th Earl of Thomond and Ulick Burke, 3rd Earl of Clanricarde. The rebels harried them as they marched into Tirawley, but the next day the Blind Abbott was injured when he chased one of Thomond's kerne – as he overtook his prey on horseback, the kerne wheeled about and struck him with a sword, nearly cutting off the foot above the ankle.
The crown forces progressed through the country, burning crops and villages, and the rebels withdrew with their cattle towards the mountains of Erris, where they soon sued for peace. Bingham was in Roscommon when the Burkes and Clandonnell accepted his conditions, which included the charges of the wars of 1586 and 1589. In 1590 Bingham's forces caused the destruction of Creevelea Abbey in County Leitrim, Moyne Abbey in Killala, County Mayo and Rosserk Friary, near Rosserk, County Mayo. He then turned against O'Rourke who had invaded Sligo in March, although illness prevented him from taking the field and his brother George assumed command. Within the month O'Rourke had fled to Ulster with his sons, and the clans of County Leitrim had submitted.