the reason why the Basmalah should not be recited at the beginning (of al-Tawbah) is that it came with the sword (i.e., the command to fight the kuffaar) and it exposes the hypocrites and their foul deeds in a manner that is not unlike any other soorah, and this theme is repeated throughout Soorat al-Tawbah.
That's the reason there. And Bismillahi Arahman Araheem means, in the name of God, most beneficent, most merciful.
An example is when we slaughter an animal, cow, sheep, chicken, etc. We don't say Bismillahi Arahman Araheem, because this isn't an act of mercy. When slaughtering an animal we just say Bismillah wa Allahu Akbar.
It means that the prophet s.a.w didn't say bismillah at the beginning of the surah, and that's the way it's remained. It's proof that the Sahaba didn't add anything when putting the Qur'an together into book form, even if they thought they saw a mistake, every surah has bismillah...you'd think they would think the surah was meant to have one aswell and put bismillah at the beginning, but they left it exactly as the prophet s.a.w recited it..not adding even a letter.
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