The Holy Qur'an consists of a 114 chapters with a common theme at the beginning of each chapter. Each chapter begins with the words "In the Name of Allah, the Beneficent, the Merciful". One would expect that all chapters begin with the aforementioned phrase, but interestingly enough, that is not the case.
The only chapter in the Holy Qur'an not to begin with Bismillah is Sura Al-Tawbah (Repentance), also known as Sura Bara'at (Dissociation). To add, the only Sura in the Qur'an to mention Bismillah twice is Sura Al-Naml, in which the holy words are mentioned at the beginning of the chapter as well as in verse 30, when Prophet Solomon addresses a letter to the Queen of Sheba: "It is from Solomon, and it begins in the name of Allah, the Beneficent, the Merciful."
This now leaves us with the question that if all other chapters in the Qur'an begin with these holy words, then why doesn't Sura Al-Tawbah? Is this by mere chance, or is there a reason behind it?
The conquest of Mecca by the Muslims was the beginning of the end of polytheism in Arabia. When the Holy Prophet and Imam Ali (peace be upon them) entered the Ka'ba and destroyed the idols that were housed there, it was the first step in eradicating polytheism that had tarnished the Holy House of Allah for years. The main aim of the revelation of Sura Al-Tawbah was to completely remove the lingering remnants of polytheism within Mecca and restore the sanctity of the Holy City. This included establishing laws that no one would be allowed to circumambulate around the Ka'ba while naked, which was a common practice in the pre-Islamic days, and that no idol worshiper would be allowed to enter the House of Allah. Since this chapter was aimed at the remaining polytheists in Mecca, there was no use of "In the name of Allah, the Beneficent, the Merciful" at the beginning of the chapter. Sura Al-Tawbah was an ultimatum from Allah to the remaining non-believers in Mecca after its fall. Since it was an ultimatum to these non-believers who were hell-bent in their opposition and enmity towards Islam, the mercy of Allah is withdrawn.
Sura Al-Tawbah is also an interesting chapter not only due to the fact that it is the only chapter not begin with Bismillah, but also because of the historical circumstances pertaining to the revelation of the Sura.
It was Hajj season, and the Holy Prophet was busy attending to issues in Medina and was unable to attend Hajj that year. That year, Abu Bakr was in charge of the pilgrims going to Mecca for Hajj. A day after the pilgrims left for Mecca, the Holy Prophet received the revelation of Sura Al-Tawbah. The Prophet was ordered that only he or one of his family members was to reveal this chapter to the pilgrims in Mecca. The Holy Prophet chose Imam Ali to convey the Sura.
"When Al-Tawbah came down to the Prophet after he had sent Abu Bakr to superintend the Hajj, someone expressed the wish that he would send it to Abu Bakr. He said: 'No one shall transmit it from me but a man of my own house.' Then he summoned Ali and said: 'Take this section from the beginning of Al-Tawbah, and proclaim it to the people on the day of sacrifice when they assemble at Mina.'" (The Life of the Messenger of God)
Sayed Ali Asghar Razwy mentions in his Restatement of the History of Islam and Muslims that the fact that Imam Ali was chosen to reveal Sura Al-Tawbah brings up two important points. One, in the absence of the Holy Prophet, Imam Ali is in charge of Islamic duties and leadership. This wasn't the first time that the Holy Prophet had chosen Imam Ali to conduct tasks that he would usually conduct himself. During the Expedition of Tabuk, in which the Holy Prophet himself led the Muslim army of 30,000 men, he left Imam Ali as the only fighting man in Medina with no troops to protect it from any attacks.
The second important point to realize is that if only Allah can decide who performs the tasks of Prophethood and gets to reveal a chapter of the Qur'an to the pilgrims in lieu of the Prophet, surely that means that only Allah will decide who will be the leader of the Muslim after the Prophet's passing!
source : www.abna.ir