He then took part in the expedition of Archibald Campbell, 9th Earl of Argyll in 1685, escaped to Holland, accompanied the Prince of Orange to England in 1688, but died at Exeter, when the troops were on the march to London.

Nominally Hamilton was in command, but the experienced officers, such as Hackston and Cleland, led the separate detachments of the Covenanters, defeating Claverhouse was due.

After the withdrawal of the government forces to Stirling the Covenanters advanced to Glasgow, where they are stated to have robbed the archbishop's house, to have pulled down the ornaments of the cathedral, and to have defaced several of the monuments, but having done so they fell back on their old position.

Sir Robert Hamilton, in name of the army, also signed a petition to Monmouth, and afterwards, when taunted with this, said that he had been ensnared into the subscription by the belief that it was Donald Cargill's work.

He ordered Hackston to retire when the bridge was attacked, and himself 'rode off with the horse' and 'allowed the foot to shift for themselves,' thus 'leaving the world to debate whether he acted most like a traitor, coward, or fool'.

Burnet, in a passage omitted from the earlier editions of his Own Time,' calls him an 'ignominious coward,' and Robert Wodrow speaks of his behaviour at Bothwell Bridge as 'ill conduct, not to say cowardice.'

At the Glorious Revolution in 1688 Hamilton returned to Scotland, and, his attainder having been reversed, succeeded in that year to the baronetcy on the death of his brother Sir William.

He was unmarried and privately took measures for securing the entailed settlement of the family inheritance on the issue of his brother's daughter Anne, by her husband Thomas, son of Sir James Oswald.

On 20 October 1686 a letter had been sent to Hamilton by the united societies stating that they had information ready to be proven 'that he had countenanced the Hamilton declaration which he and his party since had cried out so much against; that he had signed a petition to Monmouth in name of the army ; that he had received large sums of money from good people in Holland for printing the testimonies of the sufferers, and yet greater for the support of the suffering party in Scotland, of which he had given no accounts'.

Suspected of having drawn up and published the Sanquhar declaration of 18 August 1692, Hamilton was arrested at Earlstown on 10 September, and for some months he was detained a prisoner at Edinburgh and Haddington.

He was several times brought before the privy council for examination, but, although declining to acknowledge their jurisdiction or the authority of William and Mary, received his liberty on 15 May 1693, and was permitted to remain unmolested until his death, 20 October 1701.