This verse was revealed in Madinah (Mawdudi).
“O Prophet, strive against the disbelievers and the hypocrites and be harsh upon them. And their refuge is Hell, and wretched is the destination.” – Quran 66:9
Related Article: ‘Strive’ Quran 66:9
These similar words are used in Surah Tawbah (9), verse 73 (see here: “’Prophet, Fight Against The Hypocrites…’ – Surah 9:73“). This passage by no means endorses killing of innocents. The Arabic word ‘Jahid’ used here, does not necessarily mean ‘waging war’. It could be taken in a spiritual sense.
The hypocrites were never touched in the life-time of Prophet Muhammed (p), unless they actively took up arms against the Muslims. The striving against the hypocrites is with the tongue (Tafsir al-Jalalayn, Abdul Majid Daryabadi and Mawdudi). The striving against the disbelievers here refers to the Makkan Quraysh who actively oppressed and persecuted Muslims, 1400 years ago.
Furthermore, the wordings used towards end of the verse, “be harsh upon them”, shows that the Jihad against the hypocrites was with the tongue, not with the sword. Otherwise, it wouldn’t make no sense if they were killed and then told to be ‘harsh’ to them verbally. Hence, from textual point of view is that the hypocrites were dealt with the tongue i.e., rebuked.
Malik Ghulam Farid:
“3077. No advance is possible unless the disbelievers and the hypocrites are strenuously striven against. Incidentally, the verse explains the real significance of Jihad which means, ‘striving hard’. Since the hypocrites were regarded as part of the Muslim community, Jihad in the sense of fighting with the sword was never waged against them. 
“The hypocrites were a group who were outwardly a part of the Muslim community but at critical junctures they deserted the cause of Islam and showed insincerity of faith. No war was ever undertaken against them. The striving hard or jihad against them were the efforts to convince them of the truth of Islam. The same form of ‘striving’ also applies in case of the disbelievers mentioned here. More than ten English translations of the Quran render the meaning of doing Jihad in these two verses as ‘strive hard’, and not as ‘fight’ or ‘wage war’.” 
Maulana Muhammad Ali:
“Here the Prophet is commanded to carry Jihad against both unbelievers and hypocrites. The hypocrites were those who were outwardly Muslims and lived among, and were treated like, Muslims in all respects. They came to the mosque and prayed with the Muslims. They even paid the zakat. A war against them was unthinkable, and none was ever undertaken. On the other hand, they sometimes fought along with the Muslims against the unbelievers.
Therefore the injunction to carry on a jihad against both unbelievers and hypocrites could not mean the waging of war against them. It was a jihad carried on by means of the Quran as expressly stated in 25:52, a striving hard to win them over to Islam. In fact, the word is almost always used in the general sense of striving hard, including fighting where the context so requires. The following description:
‘Those who believe and those who fled [their homes] and strove hard (jahadu) in Allah’s way’ – 2:218, 8:74
Applies as much to the fighters as to those who carry on the struggle against unbelief and evil in other ways. Again, a Madinah revelation speaks together of those who exercise sabr, i.e., are steadfast or patient, and those who undertake jihad, as they are spoken of in a Makkah revelation:
‘Do you think that you will enter the Garden while Allah has not yet known those from among you who strive hard (jahadu) nor known the steadfast?’ – 3:142.” 
Scholar Abdullah Yusuf Ali:
“5545 See 9:73, where the same words introduce the argument against the Hypocrites. Here they introduce the argument against wickedness, which, though given the privilege of association with goodness and piety, persisted in wicked deeds, and in favour of those noble souls, which, though tied to wickedness, retained their purity and integrity. Two examples of each kind are given-of women, as this Surah is mainly concerned with women.”
“1331 The reference is to a plot made by the Prophet’s enemies to kill him when he was returning from Tabuk. The plot failed. It was all the more dastardly in that some of the conspirators were among the men of Madinah, who were enriched by the general prosperity that followed the peace and good government established through Islam in Madinah. Trade flourished; justice was firmly administered with an even hand. And the only return that these men could make was a return of evil for good. That was their revenge, because Islam aimed at supressing selfishness, stood for the rights of the poorest and humblest, and judged worth by righteousness rather than by birth or position.” 
Sayyid Abul Ala Maududi:
“23 For explanation, see E. N . , 82 of Surah At-Taubah:
“…In this connection, it should also be noted that this verse does not enjoin the Muslims to fight with the hypocrites. It merely meant to end the policy of leniency that had hitherto been adopted towards them. This verse enjoined that they were no more to be considered a part and parcel of the Muslim community nor were they to be allowed to take part in the management of its affairs nor consulted about any matter, so that they might not be able to spread the poison of hypocrisy. This changed policy required that the true Believers should expose all those, who adopted a hypocritical attitude and conduct and showed in any way that they were not sincere allies to Allah, His Messenger and the true Muslims. Each and every one of such hypocrites should be openly criticized and reproved so that there should remain for them no more place of honor and trust in the Muslim society: they should be socially boycotted and kept away from the consultations of the Community: their evidence in the courts of law should be regarded as untrustworthy: the doors of offices and positrons of trust should be closed against them and they should be held in contempt in the social meetings. In short; every Muslim should show by his behavior to such a one that there was no place of honor or respect or trust for a hypocrite in the Muslim society. Besides this, if any one of them was found to be guilty of treachery, there should be no connivance at his crime, nor should he be pardoned but openly tried in a court of law and should be duly punished. This Command was urgently needed at the time it came. It was obvious that in order to save the Muslim Community from fall and degradation, it was essential to purge it of all the internal dangers to its solidarity, because a Community, which nourishes hypocrites and traitors and allows the internal enemies to flourish with honor and security, wall inevitably be doomed to moral degradation and ultimate destruction. Hypocrisy is a plague and a hypocrite is the rat that carries and spreads its germs. Therefore to allow him the freedom of movement in the society is to expose the whole population to the danger of hypocrisy. Likewise, to give a place of honor and prestige to a hypocrite is to encourage many others in hypocrisy and treachery, for this shows that it is not sincerity, true faith and its welfare that count in it. One may flourish and prosper in it even if one verbally professes ;o be a Muslim and at the same time indulges in dishonesty and treachery. The Holy Prophet has expressed the same thing in a pithy saying. He said, “Whoso honors and respects the inventor of new practices which are un-Islamic, indeed helps to demolish the very structure of Islam.” 
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 The Holy Qur’an – Arabic Text With English Translation & Short Commentary By Malik Ghulam Farid, Page 1157
 Islam, Peace and Tolerance [Copyright 2006] By Zahid Aziz, page 45
 A Handbook of Islam: An Abridged Edition of ‘The Religion of Islam’  By Maulana Muhammad Ali, page 307 – 308
 The Meaning Of the Glorious Qur’an: Text, Translation, and Commentary by Abdullah Yusuf Ali, page 121 and 408 https://bradfordisoc.files.wordpress.com/2010/07/quran-yusuf-ali.pdf
 Sayyid Abul Ala Maududi – Tafhim al-Qur’an – The Meaning of the Qur’an