In the name of Allah, the Beneficent, the Merciful
There are a few interpretations for the reason the bismillah (“in the name of Allah, the Gracious, the Merciful”) is not written at the beginning of Surah al-Tawbah.
One reason is that the surah discusses the idolaters who showed aggression against the Muslims and continually violated their peace treaties. Muslims were commanded to fight them in self-defense, so it is believed the bismillah is not written because mercy has been removed from these people. This is the interpretation of some scholars but it not authentically attributed to the Prophet, peace and blessings be upon him, that he interpreted the surah this way.
In my view, the strongest opinion based upon an authentic narration is that the bismillah is not written because when the companions were compiling the Quran, it was not clear to them if Surah At-Tawbah was its own separate surah or if it was a continuation of Surah Al-Anfal.
Ibn Abbas said to Uthman:
مَا حَمَلَكُمْ أَنْ عَمَدْتُمْ إِلَى الْأَنْفَالِ وَهِيَ مِنْ الْمَثَانِي وَإِلَى بَرَاءَةٌ وَهِيَ مِنْ الْمِئِينَ فَقَرَنْتُمْ بَيْنَهُمَا وَلَمْ تَكْتُبُوا بَيْنَهُمَا سَطْرَ بِسْمِ اللَّهِ الرَّحْمَنِ الرَّحِيمِ وَوَضَعْتُمُوهَا فِي السَّبْعِ الطُّوَلِ مَا حَمَلَكُمْ عَلَى ذَلِكَ
What is your reasoning with Surah Al-Anfal, which has less than a hundred verses, and Surah At-Tawbah, which has more than a hundred verses, yet you put them together without writing in the name of Allah, the Most Gracious, the Most Merciful between them and you placed them with the seven long surahs. Why did you do that?
Uthman, may Allah be pleased with him, said:
الْأَنْفَالُ مِنْ أَوَائِلِ مَا أُنْزِلَتْ بِالْمَدِينَةِ وَكَانَتْ بَرَاءَةٌ مِنْ آخِرِ الْقُرْآنِ وَكَانَتْ قِصَّتُهَا شَبِيهَةً بِقِصَّتِهَا فَظَنَنْتُ أَنَّهَا مِنْهَا فَقُبِضَ رَسُولُ اللَّهِ صَلَّى اللَّهُ عَلَيْهِ وَسَلَّمَ وَلَمْ يُبَيِّنْ لَنَا أَنَّهَا مِنْهَا فَمِنْ أَجْلِ ذَلِكَ قَرَنْتُ بَيْنَهُمَا وَلَمْ أَكْتُبْ بَيْنَهُمَا سَطْرَ بِسْمِ اللَّهِ الرَّحْمَنِ الرَّحِيمِ فَوَضَعْتُهَا فِي السَّبْعِ الطُّوَلِ
Al-Anfal was among the first to be revealed in Medina and At-Tawbah was among the last of those revealed of the Quran and their discussions resemble each other, so we thought that they were part of each other. Then the Messenger of Allah died and it was not clear to us if they were part of each other. For this reason, we put them together without writing in the name of Allah, the Most Gracious, the Most Merciful and we included them with the seven long surahs.
Source: Sunan At-Tirmidhi 3086, Grade: Sahih
This is an authentic report which settles the question clearly. It is not correct, then, to say all the surahs of the Quran begin with bismillah besides At-Tawbah, because the companions acknowledged that At-Tawbah could be part of Al-Anfal, in which case every surah would begin with the bismillah.
Besides this, there are a few other reasons this interpretation is preferred.
First, it should make clear that the verses of Surah At-Tawbah do not contradict or abrogate the verses of Surah Al-Anfal. Al-Anfal commands Muslims to make peace with those who offer them peace.
وَإِن جَنَحُوا لِلسَّلْمِ فَاجْنَحْ لَهَا وَتَوَكَّلْ عَلَى اللَّهِ ۚ إِنَّهُ هُوَ السَّمِيعُ الْعَلِيمُ
If they incline to peace, then incline to it also and rely upon Allah. Verily, it is He who is the Hearing, the Knowing.
Surah Al-Anfal 8:61
Therefore, the verses of Surah At-Tawbah do not negate this command.
Second, the verses of Surah At-Tawbah still offer mercy and forgiveness to the idolaters who give up their fight against the Muslims.
وَإِنْ أَحَدٌ مِّنَ الْمُشْرِكِينَ اسْتَجَارَكَ فَأَجِرْهُ حَتَّىٰ يَسْمَعَ كَلَامَ اللَّهِ ثُمَّ أَبْلِغْهُ مَأْمَنَهُ ۚ ذَٰلِكَ بِأَنَّهُمْ قَوْمٌ لَّا يَعْلَمُونَ
If any one of the idolaters seeks your protection, then grant him protection so that he may hear the words of Allah. Then deliver him to his place of safety. That is because they are a people who do not know.
Surah At-Tawbah 9:6
Any idolater who wanted to make peace with the Muslims was given that opportunity. This is because the mercy of Allah is given to all those who seek it.
We should not interpret the missing bismillah as an abrogation of Allah’s mercy or command to make peace. Rather, mercy and peace are consistent themes throughout the Quran and Sunnah, so we should not make an excuse to abandon them.
Success comes from Allah, and Allah knows best.