Punishment under itmam-e-hujjat did not come in one piece, rather it came in two prominent episodes. The first episode of the punishment was implmented during Badr (ghazwa-e-Badr) where all the prominent leaders of Quresh were killed and that is why Quran calls it Youm-ul-Furqan. The second and final episode of the punishment was implemented when Surah Tauba was revealed. Surah Tauba itself was revealed in six different installments. Following is the summary of the verses revealed in those six installments which is extracted from the subject-matter availabe in those verses.
First Installment: Verses 1 to 12 (Revealed after Covenant of Hudaibiya and at time when Quresh had not violated the terms of the agreement yet)
Second Installment: Verses 13 to 22 (Revealed after Quresh had violated the terms of the agreement somewhere around 8th Hijri)
Third Installment: Verses 23 to 37 (Revealed around 9th Hijri before the prophesied Hajj where final accouncement as mentioned in the Verse 3 was still due)
Fourth Installment: Verses 38 to 72 (Revealed at a time when Prophet Muhammad was preparing for Ghazwa-e-Tabuk during 9th Hijri)
Fifth Installment: Verses 73 to 112 (Revealed during Tabuk expedition or on return from Tabuk)
Sixth Installment: Verses 113 to 129 (Revealed sometime on Medina after Prophet (sws) had already returned from Tabuk)
– Following would be the chronological order of the last episode of divine punishemnt as per Surah Tauba:
First the ultimatum of four months was given to the nearby tribes (the ones to whom this information could have reached easily) and action was initialted after four months has lapsed. This period lies somewhere after covenant of Hudaibiya (around 6th to 8th Hijri). During 8th Hijri, after violation of the pact by Quresh, Mecca was also conquered. In the conquest of Mecca, except for a few Brutal Adversaries (Muanideen), general amnesty was declared and people came into folds of Islam in high numbers, so there was no major blood shed in Mecca. Then in 9th Hijri, the final announcement was made during Hajj under leadership of Abu Bakr where all the tribes of Arab were addressed and the final punishment was announced for the whole of Arabia. After expiration of the next 50 days after Hajj (i.e. the end of Haram months), the prophet (sws) sent many expeditions to either demolish the polytheistic centers found in the land of Arabia or to give option to the tribes who had not yet accepted Islam to either accept it or face death. Many tribes accepted Islam during this time and many were killed as well, but the exact number of people who were killed because of this punishment cannot be known with certainty.
For more details, please read the first portion (Pages 11 to 66) of the book “Jihad” by Mr. Ammar Khan Nasir (Attached with this response).