Whilst in London, Gaughan became a member of the Official IRA (OIRA) through its English wing Clann na hEirreann and became an IRA volunteer in a London-based active service unit. In December 1971, he was sentenced at the Old Bailey to seven years prison for his part in an IRA fundraising mission to rob a bank in Hornsey, north London, which yielded just £530, and for the possession of two revolvers.
Gaughan was initially sent to Wormwood Scrubs, where he spent two years before being transferred to the top security Albany Prison on the Isle of Wight. Whilst at Albany Prison, Gaughan requested political status; this was refused, and he was then put in solitary confinement. He was later transferred to Parkhurst Prison, where four of the Belfast Ten were on hunger strike for political status.
On 31 March 1974, Gaughan, along with Paul Holme, Hugh Feeney and fellow Mayoman Frank Stagg, went on hunger strike to support the fight of Dolours and Marion Price to obtain political status and to be transferred to a jail in Ireland. The prisoners demands were as follows.
After visiting Michael in jail, his brother John described his condition: "His throat had been badly cut by force feeding and his teeth loosened. His eyes were sunken, his cheeks hollow and his mouth was gaping open. He weighed about six stone."
During his hunger strike, his weight dropped from 160 lb to 84 lb Gaughan was force-fed from 22 April and this occurred 17 times during course of his hunger strike. The last time he was force-fed was the night before his death on Sunday 2 June. After a hunger strike that lasted 64 days, he died on Monday 3 June 1974, aged 24 years old.
The cause of his death was disputed. The British government stated that he died of pneumonia; the Gaughan family stated that he died after prison doctors injured him fatally when food lodged in a lung punctured by a force-feeding tube.
Gaughan's death caused controversy in English medical circles as doctors were unsure whether or not they should give medical treatment to a patient, some forms of treatment can be classed as assault if given without the express permission of the patient.
The timing of his death came just one week after the British Government had capitulated to the demands of Loyalist hunger strikers' demands. After his death, the British government's policy of force-feeding ended, and the remaining hunger strikers were given assurances that they would be repatriated to Irish prisons. However, these promises were reneged on by the British government.
His death is referenced in the song "Take me Home to Mayo," also known as "The Ballad of Michael Gaughan," composed by Seamus Robinson and has been performed and recorded by many Irish musicians including Christy Moore, the Wolfe Tones and Derek Warfield and the Dublin City Ramblers.
Gaughan's body was initially removed from London and on Friday, 7 June, and on Saturday, 8 June 1974, over 3,000 mourners lined the streets of Kilburn and marched behind his coffin, which was flanked by an IRA honour guard, to a requiem mass held in the Church of the Sacred Heart of Jesus in Kilburn.
On Saturday, his body was transported to Dublin, where again it was met by mourners and another IRA guard of honour who brought it to the Adam and Eve's Franciscan church on Merchant's Quay, where thousands filed past as it lay in state. The following day, his body was removed to Ballina, County Mayo. The funeral mass took place on 9 June, at St. Muredach's Cathedral, Ballina, and the procession then led to Leigue Cemetery, Ballina. Gaughan was given a full republican burial and was laid to rest in the Republican plot, where Frank Stagg would also join him after being reburied in November 1976. His funeral was attended by over 50,000 people and was larger than the funeral of former Irish president Eamon de Valera.
Mayo Republican Jackie Clarke (Irish name: Seán Ó Clérigh) presided at the last obsequies, and the oration at his graveside was given by Dáithí Ó Conaill, who stated that Gaughan had "been tortured in prison by the vampires of a discredited empire who were joined by decrepit politicians who were a disgrace to the name of Irishmen".
His coffin was drapped in the same Tricolour that was used for Terence McSwiney's funeral 54 years earlier, the same flag would later be used in the funeral of James McDade who was a IRA member killed in a premature explosion in Coventry.