When the rioters showed the letter written on his behalf, 'Uthmaan bin 'Affaan, may Allah be pleased with him, declared it a forgery. ‘Abdur-Rahmaan bin ‘Udays, the ringleader of the rioters rejected it saying: "If you are a liar, you are not fit to remain as a Caliph. In case you are true in your claim, then such a weak Caliph should not be left to rule if he is not able to keep control over his administration and lets anybody write anything on his behalf." At last, ‘Abdur-Rahmaan bin 'Udays asked 'Uthmaan bin 'Affaan to quit the Caliphate. However, he said: "I can't put off the garment that Allah has caused me to put on." That is, he refused to give up the post of the Caliph.

When the intensity of the siege increased and even the supply of water was stopped, 'Uthmaan bin 'Affaan went to the roof of his house and reminded them of his sacrifices for Islam and the position he held after embracing Islam. A section of the rioters seemed to forgive him but Maalik bin Al-Ashtar intervened to keep them firm in their plan. Moreover, when the rioters were convinced of the arrival of rescue forces from the provinces, they determined to do away with the Caliph.

During these days, 'Aa’ishah, may Allah be pleased with her, decided to go on Hajj. She sent for Muhammad bin Abu Bakr to accompany her on the journey to Makkah. But he refused to do so, because he was involved with the rioters. Hanthalah, may Allah be pleased with him, the scribe of the Revelations, said to him: "You refuse to accompany the Mother of the Believers and instead follow the fools of Arabia." Muhammad bin Abu Bakr gave no reply. Talhah and Az-Zubayr, may Allah be pleased with them, had closed their doors and would neither go anywhere nor meet anybody. Ibn 'Abbaas, may Allah be pleased with him, faced the rioters at the door of 'Uthmaan bin 'Affaan and stopped them from drawing near. However, the Caliph insisted that he would lead the Hajj caravan, although he said that waging Jihaad against the rioters was to him better than performing the Hajj. Al-Hasan bin 'Ali, 'Abdullaah bin Az-Zubayr, Muhammad bin Talhah and Sa'eed bin Al-'Aas, may Allah be pleased with them, stopped the rioters from opening the door and fought to push them back.

However, 'Uthmaan bin 'Affaan, may Allah be pleased with him, prevented them from doing so on oath and called them in. When the rioters set fire to the doors, they fought and drove them out once again. 'Uthmaan bin 'Affaan was then reciting the Quran. When he reached the verse (which means): "Those to whom people (i.e. hypocrites) said: 'Indeed, the people have gathered against you, so fear them.' But it (merely) increased them in faith, and they said: ' Sufficient for us is Allah, and (He is) the best Disposer of affairs.’" [Quran 3:173]

He, may Allah be pleased with him, said addressing those present: "The Messenger of Allah, has taken a pledge from me and I firmly keep it, so hold yourselves back from fighting the rioters." He also asked Al-Hasan bin 'Ali, may Allah be pleased with him, to go back to his father, but he declined the advice and kept at the door.

Al-Mugheerah bin Al-Akhnas, may Allah be pleased with him, could not bear the situation, attacked the rioters along with some of his companions and was martyred. In the same way, Abu Hurayrah, may Allah be pleased with him, launched an assault on the rioters reciting the verse (which means): "And O my people, how is it that I invite you to salvation while you invite me to the Fire?" [Quran 40:41]

When 'Uthmaan, may Allah be pleased with him, came to know of it, he insistently called him back.

Meanwhile, 'Abdullaah bin Salaam, may Allah be pleased with him, came and did all he could to pacify the rioters, but in vain. Among those present with 'Uthmaan bin 'Affaan, some were upstairs watching the movements of the rioters while others were at the gate stopping their entry. 'Uthmaan bin 'Affaan and his wife Naa'ilah, the daughter of Al-Furafisah, may Allah be pleased with them, were inside.

The rioters scaled the walls, entered the house of 'Uthmaan bin 'Affaan, and made an assault on him. First of all Muhammad bin Abu Bakr came near 'Uthmaan bin 'Affaan, may Allah be pleased with him, and said catching hold of his beard: "O long-bearded one, may Allah put you to disgrace." 'Uthmaan, may Allah be pleased with him, replied: "I am not a long-bearded man, but 'Uthmaan, the Chief of the Believers." Thereupon Muhammad bin Abu Bakr angrily said: "You covet the Caliphate even in your old age." 'Uthmaan, may Allah be pleased with him, said: "Had your father been alive, he would have valued my old age." At this Muhammad bin Abu Bakr got ashamed and left. Followed by his retreat a group of criminals came down scaling the wall. The group included ‘Abdur-Rahmaan bin 'Udays, 'Amr bin Hamiq, 'Umayr bin Jannabi, Sudan bin Humraan, Al-Ghaafiqi and Kinaanah bin Bishr, who first struck 'Uthmaan, may Allah be pleased with him, with a sword. His wife Naa'ilah came forward and stretched her hand to stop the stroke, with the result that her fingers were cut off and thrown away. However, he struck 'Uthmaan, may Allah be pleased with him, a second time, which led to his martyrdom. It so happened when 'Uthmaan, may Allah be pleased with him, was reciting the Quran, his blood dropped on the verse (which means): "…. and Allah  will be sufficient for you against them. And He is the Hearing, the Knowing." [Quran 2:137]

'Amr bin Hamiq gave him nine wounds with his spear. 'Umayr bin Jannabi moved forward and kicked him violently more than once, so that his ribs were broken. At every kick he would say: "It was you who had imprisoned my father and the poor man died in captivity." Naa'ilah called out to those upstairs who were unaware of what was happening in the house. The rioters had completed their evil act before those upstairs arrived. The criminals fled and the slaves of 'Uthmaan killed a few of them.

Nobody was needed now to guard the door. The rioters then made a forced entry into the house and plundered all the articles that they found. The news of this tragedy spread like lightning. This soul-shattering incident came to pass on Friday, Thul-Hijjah 18, 35 AH. The dead body of 'Uthmaan laid unshrouded and unburied for three days. At last Haakim bin Hizaam and Jubayr bin Mut'im, may Allah be pleased with them, went to 'Ali, may Allah be pleased with him, and he gave permission for him to be buried. The body was buried between Maghrib and Isha' prayers. Az-Zubayr, Hasan, Abu Jahm bin Huthayfah, and Marwaan, may Allah be pleased with them, accompanied the bier. The rioters tried to obstruct the burial service but held back on the intervention of 'Ali. Jubayr bin Mut'im led the funeral prayers. He was then buried without bath and coffin.

'Uthmaan bin 'Affaan, may Allah be pleased with him, died at the age of 82 after passing 12 years as a Caliph. He was buried in Jannat-ul-Baqi' leaving behind eleven sons and six daughters.