Overall meaning : Allah Almighty tells us here about another group of hypocrites who built a mosque in Madeenah to cause harm to the believers and in opposition to them and to their mosque in which they assembled, to propagate disbelief in Allah, Glorified and Exalted be He, to foment division among the believers and to provide an outpost for those who have already been warring against Allah and His Messenger. He further indicates that, in addition to these evil intentions, they will still swear to you, believers, that they had the best of intentions, but Allah bears witness that they are certainly liars.
Allah then forbids His Prophet, may Allah bless him and grant him peace, to pray in the mosque built by the hypocrites at any time, stating that it is more fitting that he should pray in the mosque that was founded from the very first day upon fear of, and obedience to, Allah; for in it are men who love to purify and cleanse themselves of filth and sins, and Allah loves those who purify themselves.
The Almighty then points out that those who erect their structure upon the fear of, and obedience to, Allah Almighty and those who erect theirs on the edge of a crumbling pit that crumbles down along with the structure and its builder into the fire of Hell are by no means equal, and Allah does not guide the wrongdoers.
He also asserts that the mosque the hypocrites built to sow dissension among Muslims will continue to be a source of doubt and hypocrisy in their hearts until their hearts are torn to pieces and die in that state. Allah is All-Knowing, All-Wise.