It has been alleged by an Islam and Muslim hating missionary that there are a number of passages in the Qur’an which indicate that Islam is not a monotheistic religion and that there are a number of verses which indicate so.
Let us examine the verses claimed to contradict monotheism.
That is Jesus, the son of Mary – the word of truth about which they are in dispute. It is not [befitting] for Allah to take a son; exalted is He! When He decrees an affair, He only says to it, “Be,” and it is. “And indeed, Allah is my Lord and your Lord, so worship Him. That is a straight path.” 
It is claimed that since the speaker at the start is Allah, hence the ending words are also the words of Allah i.e. it is Allah who is saying And indeed, Allah is my Lord and your Lord, so worship Him which would indicate that Allah is referring to someone else as Allah and His Lord. If only the selected passage is seen as it is, the outcome would most certainly appear to be as claimed. However, one needs to see the context as well. Let us understand these verses again with the context i.e. by selecting a few preceding verses.
[Jesus] said, “Indeed, I am the servant of Allah. He has given me the Scripture and made me a prophet. And He has made me blessed wherever I am and has enjoined upon me prayer and zakah (obligatory charity) as long as I remain alive And [made me] dutiful to my mother, and He has not made me a wretched tyrant. And peace is on me the day I was born and the day I will die and the day I am raised alive.” 
The passage quoted here immediately comes before the first passage quoted above. Here we see that it was Prophet Eisa (Jesus) (عليه السلام) who was the one speaking. As soon as it is mentioned that he spoke in the cradle, the following verse mentions that this is the truth about Prophet Eisa (Jesus) (عليه السلام) about which they doubt. In other words, the miracle of the cradle is mentioned followed by a clarification from Allah about the truth. Then that truth is further explained in the next verse as to how Allah decrees an affair. Then when the matter is stated and explained, the context goes back to the speech of Prophet Eisa (Jesus) (عليه السلام) where he states And indeed, Allah is my Lord and your Lord, so worship Him. Notice that the words of Prophet Eisa (Jesus) (عليه السلام) in both the passages above start with Indeed. His sentence starts with Indeed, I am the servant of Allah followed by clarification and explanation from Allah and then again the words of Prophet Eisa (Jesus) (عليه السلام) continue with And indeed, Allah is my Lord and your Lord, so worship Him.
It does not require too much of a brain to understand the way of explaining here. The context and the words of Prophet Eisa (Jesus) (عليه السلام) themselves clarify who the speaker is in each verse.
There are similar passages in the Qur’an where an incident or event is mentioned preceded by a break to explain that incident or event and then continuing back with that incident or event and therefore the passages quoted above are not an exception. The only way to find problems in them is to look at them out of context in isolation.
“And we descend not except by the order of your Lord. To Him belongs that before us and that behind us and what is in between. And never is your Lord forgetful. 
It is argued that since the entire Qur’an is the word of Allah in first person and there not being a mention of someone else’s speech before the above quoted verse, the speaker is Allah and He describes His own descending by the order of the Lord of Prophet Muhammad (ﷺ) who is other than Allah. They argue that the structure of the sentence is in such a way that this is the only conclusion derived from the verse.
To assume that this is the only and correct conclusion derived from this verse would be trickery. For the Qur’an, the entire book is the context. If a matter has been established somewhere in the Qur’an, then that cannot be ignored in other parts of the Qur’an. The Qur’an explicitly establishes that the Lord of Prophet Muhammad (ﷺ) is none other than Allah.
The unbelievers _ be they among the people of the scriptures, or among the idolaters _ would not like to see any blessings ever conferred upon you by your Lord. But, for His mercy Allah selects whom He wants. Allah is the Lord of Infinite Grace and Bounties! 
(Tell them), “Are you going to argue with us concerning Allah? He is our Lord, and your Lord! We have our deeds, and you have yours to account for. We have devoted ourselves (exclusively) to Him.” 
That definitely is the truth from your Lord. Allah is not unaware of anything you do. 
“Truly! Allah is my Lord, and your Lord! Therefore, worship Him (alone); that is the straight path!” 
This message is repeated hundreds of times in the Qur’an. If this is kept in mind while understanding the verse in question, no one would arrive at the faulty conclusion that there is a Lord other than Allah or that Allah Himself has a Lord.
Another question that may arise could be that how one can be sure that those that descend are the angels as the text is ambiguous. As has been explained before, the entire Qur’an is the context. When that is kept in mind, there appears no confusion, contradiction or ambiguity. The Qur’an states:
The angels and the Spirit (Jibreel) descend therein by permission of their Lord for every matter.
And we descend not except by the order of your Lord are the words of Angel Jibreel. The sentence takes a grammatical shift. Grammatical shift or Iltifāt is a feature of the Arabic language.  The concept requires a separate topic for explanation and the link is highly recommended.
Imam Ahmad recorded that Ibn `Abbas said that the Messenger of Allah said to Jibril,
«مَا يَمْنَعُكَ أَنْ تَزُورَنَا أَكْثَرَ مِمَّا تَزُورُنَا؟»
(What prevents you from visiting us more than you do) Then this Ayah was revealed,
﴿وَمَا نَتَنَزَّلُ إِلاَّ بِأَمْرِ رَبِّكَ﴾
(And we descend not except by the command of your Lord.) Al-Bukhari was alone in recording it and he related it with the Tafsir of this Ayah. Al-`Awfi reported from Ibn `Abbas that he said, “Jibril was kept from visiting the Messenger of Allah , so he was disturbed and grieved because of this. Then, Jibril came to him and said, `O Muhammad,
﴿وَمَا نَتَنَزَّلُ إِلاَّ بِأَمْرِ رَبِّكَ﴾
(And we descend not except by the command of your Lord.)”’
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