The Almighty Allah says in the Qur’an:

kill them wherever you find them… (Al-Baqarah 2:191)

There is a  misconception regarding this verse as many non-Muslims claim that the Qur’an teaches violence and encourages fighting and killing them wherever they are. We Muslims say that this a historical event which took place at the time of the Prophet (peace be upon him) when he and his companions were tortured and prosecuted to a great degree from the disbelievers of Makkah, yet the Almighty Allah did not allow them to retaliate.

Later He revealed verses allowing Muslims to fight them as they fought Muslims before. These verses were addressed to the Prophet and not a permission for us to kill them nowadays.

In this talk, Dr. Zakir Naik refutes this misconception  and how non-Muslims quote the verses and hadiths out of their contexts.