This is the famous verse from Quran that orders us to obey Allah and obey the messenger, before misunderstanding this verse or submit to what Allah wants us to really obey, we should go through the context of this verse. This context analysis of this above verse will help us to understand the command of our GOD.

Verse 4:59

 يَا أَيُّهَا ٱلَّذِينَ آمَنُواْ أَطِيعُواْ ٱللَّهَ وَأَطِيعُواْ ٱلرَّسُولَ وَأُوْلِي ٱلأَمْرِ مِنْكُمْ فَإِن تَنَازَعْتُمْ فِي شَيْءٍ فَرُدُّوهُ إِلَى ٱللَّهِ وَٱلرَّسُولِ إِن كُنْتُمْ تُؤْمِنُونَ بِٱللَّهِ وَٱلْيَوْمِ ٱلآخِرِ ذٰلِكَ خَيْرٌ وَأَحْسَنُ تَأْوِيلاً 

O you who believe obey God and obey the Messenger and those in authority among you that is rulers when they command you to obey God and His Messenger. If you should quarrel disagree about anything refer it to God that is to His Book and the Messenger while he lives and thereafter refer to his Sunna in other words examine these disputes with reference to these two sources if you believe in God and the Last Day; that reference to the two sources is better for you than quarrelling or adhering to personal opinions and more excellent in interpretation in the end.

Context of the above verse:

4:58

إِنَّ ٱللَّهَ يَأْمُرُكُمْ أَن تُؤدُّواْ ٱلأَمَانَاتِ إِلَىۤ أَهْلِهَا وَإِذَا حَكَمْتُمْ بَيْنَ ٱلنَّاسِ أَن تَحْكُمُواْ بِٱلْعَدْلِ إِنَّ ٱللَّهَ نِعِمَّا يَعِظُكُمْ بِهِ إِنَّ ٱللَّهَ كَانَ سَمِيعاً بَصِيراً

Talal Itani

God instructs you to give back things entrusted to you to their owners. And when you judge between people, judge with justice. God’s instructions to you are excellent. God is All-Hearing, All-Seeing.
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Verse 4:69

وَمَن يُطِعِ اللَّهَ وَالرَّسُولَ فَأُولَٰئِكَ مَعَ الَّذِينَ أَنْعَمَ اللَّهُ عَلَيْهِم مِّنَ النَّبِيِّينَ وَالصِّدِّيقِينَ وَالشُّهَدَاءِ وَالصَّالِحِينَ ۚ وَحَسُنَ أُولَٰئِكَ رَفِيقًا

Whoever obey God and obey the Messenger —these are with those whom God has blessed—among the prophets, and the sincere, and the martyrs, and the upright. Excellent are those as companions.

Context of the above verse:

4:64-68

وَمَا أَرْسَلْنَا مِن رَّسُولٍ إِلَّا لِيُطَاعَ بِإِذْنِ اللَّهِ ۚ وَلَوْ أَنَّهُمْ إِذ ظَّلَمُوا أَنفُسَهُمْ جَاءُوكَ فَاسْتَغْفَرُوا اللَّهَ وَاسْتَغْفَرَ لَهُمُ الرَّسُولُ لَوَجَدُوا اللَّهَ تَوَّابًا رَّحِيمًافَلَا وَرَبِّكَ لَا يُؤْمِنُونَ حَتَّىٰ يُحَكِّمُوكَ فِيمَا شَجَرَ بَيْنَهُمْ ثُمَّ لَا يَجِدُوا فِي أَنفُسِهِمْ حَرَجًا مِّمَّا قَضَيْتَ وَيُسَلِّمُوا تَسْلِيمًاوَلَوْ أَنَّا كَتَبْنَا عَلَيْهِمْ أَنِ اقْتُلُوا أَنفُسَكُمْ أَوِ اخْرُجُوا مِن دِيَارِكُم مَّا فَعَلُوهُ إِلَّا قَلِيلٌ مِّنْهُمْ ۖ وَلَوْ أَنَّهُمْ فَعَلُوا مَا يُوعَظُونَ بِهِ لَكَانَ خَيْرًا لَّهُمْ وَأَشَدَّ تَثْبِيتً﴿وَإِذًا لَّآتَيْنَاهُم مِّن لَّدُنَّا أَجْرًا عَظِيمًاوَلَهَدَيْنَاهُمْ صِرَاطًا مُّسْتَقِيمًا

Talal Itani

We did not send any messenger except to be obeyed by God’s leave. Had they, when they wronged themselves, come to you, and prayed for God’s forgiveness, and the Messenger had prayed for their forgiveness, they would have found God Relenting and Merciful. But no, by your Lord, they will not believe until they call you to arbitrate in their disputes, and then find within themselves no resentment regarding your decisions, and submit themselves completely. Had We decreed for them: “Kill yourselves,” or “Leave your homes,” they would not have done it, except for a few of them. But had they done what they were instructed to do, it would have been better for them, and a firmer confirmation. And We would have given them from Our presence a rich compensation. And We would have guided them on a straight path.
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Verse 5:92

وَأَطِيعُواْ ٱللَّهَ وَأَطِيعُواْ ٱلرَّسُولَ وَٱحْذَرُواْ فَإِن تَوَلَّيْتُمْ فَٱعْلَمُوۤاْ أَنَّمَا عَلَىٰ رَسُولِنَا ٱلْبَلاَغُ ٱلْمُبِينُ

And obey God and obey the Messenger and beware of disobedient acts; but if you turn away from obedience then know that Our Messenger’s duty is only to proclaim plainly to convey clearly the Message — your requital falls on Us.

Context of the above verse:

5: 90 – 91

 يَٰأَيُّهَا ٱلَّذِينَ آمَنُواْ إِنَّمَا ٱلْخَمْرُ وَٱلْمَيْسِرُ وَٱلأَنصَابُ وَٱلأَزْلاَمُ رِجْسٌ مِّنْ عَمَلِ ٱلشَّيْطَانِ فَٱجْتَنِبُوهُ لَعَلَّكُمْ تُفْلِحُونَ إِنَّمَا يُرِيدُ ٱلشَّيْطَانُ أَن يُوقِعَ بَيْنَكُمُ ٱلْعَدَاوَةَ وَٱلْبَغْضَآءَ فِي ٱلْخَمْرِ وَٱلْمَيْسِرِ وَيَصُدَّكُمْ عَن ذِكْرِ ٱللَّهِ وَعَنِ ٱلصَّلاَةِ فَهَلْ أَنْتُمْ مُّنتَهُونَ

Talal Itani:

O you who believe! Intoxicants, gambling, idolatry, and divination are abominations of Satan’s doing. Avoid them, so that you may prosper. Satan wants to provoke strife and hatred among you through intoxicants and gambling, and to prevent you from the remembrance of God, and from prayer. Will you not desist?

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Verse 8:20

يَا أَيُّهَا الَّذِينَ آمَنُوا أَطِيعُوا اللَّهَ وَرَسُولَهُ وَلَا تَوَلَّوْا عَنْهُ وَأَنْتُمْ تَسْمَعُونَ

O you who believe! obey God and obey his Messenger, and do not turn away from him when you hear.

Context of the above verse:

8 : 15 – 21

يَا أَيُّهَا الَّذِينَ آمَنُوا إِذَا لَقِيتُمُ الَّذِينَ كَفَرُوا زَحْفًا فَلَا تُوَلُّوهُمُ الْأَدْبَارَوَمَن يُوَلِّهِمْ يَوْمَئِذٍ دُبُرَهُ إِلَّا مُتَحَرِّفًا لِّقِتَالٍ أَوْ مُتَحَيِّزًا إِلَىٰ فِئَةٍ فَقَدْ بَاءَ بِغَضَبٍ مِّنَ اللَّهِ وَمَأْوَاهُ جَهَنَّمُ ۖ وَبِئْسَ الْمَصِيرُفَلَمْ تَقْتُلُوهُمْ وَلَٰكِنَّ اللَّهَ قَتَلَهُمْ ۚ وَمَا رَمَيْتَ إِذْ رَمَيْتَ وَلَٰكِنَّ اللَّهَ رَمَىٰ ۚ وَلِيُبْلِيَ الْمُؤْمِنِينَ مِنْهُ بَلَاءً حَسَنًا ۚ إِنَّ اللَّهَ سَمِيعٌ عَلِيمٌذَٰلِكُمْ وَأَنَّ اللَّهَ مُوهِنُ كَيْدِ الْكَافِرِينَإِن تَسْتَفْتِحُوا فَقَدْ جَاءَكُمُ الْفَتْحُ ۖ وَإِن تَنتَهُوا فَهُوَ خَيْرٌ لَّكُمْ ۖ وَإِن تَعُودُوا نَعُدْ وَلَن تُغْنِيَ عَنكُمْ فِئَتُكُمْ شَيْئًا وَلَوْ كَثُرَتْ وَأَنَّ اللَّهَ مَعَ الْمُؤْمِنِينَيَا أَيُّهَا الَّذِينَ آمَنُوا أَطِيعُوا اللَّهَ وَرَسُولَهُ وَلَا تَوَلَّوْا عَنْهُ وَأَنتُمْ تَسْمَعُونَوَلَا تَكُونُوا كَالَّذِينَ قَالُوا سَمِعْنَا وَهُمْ لَا يَسْمَعُونَ

Talal Itani:

O you who believe! When you meet those who disbelieve on the march, never turn your backs on them. Anyone who turns his back on them on that Day, except while maneuvering for battle, or to join another group, has incurred wrath from God, and his abode is Hell—what a miserable destination! It was not you who killed them, but it was God who killed them. And it was not you who launched when you launched, but it was God who launched. That He may bestow upon the believers an excellent reward. God is Hearing and Knowing. Such is the case. God will undermine the strategy of the disbelievers. If you desire a verdict, the verdict has come to you. And if you desist, it would be best for you. And if you return, We will return; and your troops, however numerous, will not benefit you. God is with the believers. O you who believe! Obey God and His Messenger, and do not turn away from him when you hear. Do not be like those who say, “We hear,” but pay no heed to what they hear

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Verse 24:54

 قُلْ أَطِيعُواْ ٱللَّهَ وَأَطِيعُواْ ٱلرَّسُولَ فَإِن تَوَلَّوْاْ فَإِنَّمَا عَلَيْهِ مَا حُمِّلَ وَعَلَيْكُمْ مَّا حُمِّلْتُمْ وَإِن تُطِيعُوهُ تَهْتَدُواْ وَمَا عَلَى ٱلرَّسُولِ إِلاَّ ٱلْبَلاَغُ ٱلْمُبِينُ

Say, “Obey God and obey the Messenger.” But if they turn away, then he is responsible for his obligations, and you are responsible for your obligations. And if you obey him, you will be guided. It is only incumbent on the Messenger to deliver the Clarifying Message.

Context of the above verse:

24 : 47-53

Talal Itani:

And they say, “We have believed in God and the Messenger, and we obey,” but some of them turn away afterwards. These are not believers. And when they are called to God and His Messenger, in order to judge between them, some of them refuse. But if justice is on their side, they accept it willingly. Is there sickness in their hearts? Or are they suspicious? Or do they fear that God may do them injustice? Or His Messenger? In fact, they themselves are the unjust. The response of the believers, when they are called to God and His Messenger in order to judge between them, is to say, “We hear and we obey.” These are the successful. Whoever obeys God and His Messenger, and fears God, and is conscious of Him—these are the winners.
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Verse 47:33

 يٰأَيُّهَا ٱلَّذِينَ آمَنُوۤاْ أَطِيعُواْ اللَّهَ وَأَطِيعُواْ ٱلرَّسُولَ وَلاَ تُبْطِلُوۤاْ أَعْمَالَكُم

O you who believe! , “Obey God and obey the Messenger.” and obey the Messenger, and do not let your deeds go to waste.

Context of the above verse:

47 : 31-32

 إِنَّ ٱلَّذِينَ كَفَرُواْ وَصَدُّواْ عَن سَبِيلِ ٱللَّهِ وَشَآقُّواْ ٱلرَّسُولَ مِن بَعْدِ مَا تَبَيَّنَ لَهُمُ ٱلْهُدَىٰ لَن يَضُرُّواْ ٱللَّهَ شَيْئاً وَسَيُحْبِطُ أَعْمَالَهُمْ وَلَنَبْلُوَنَّكُمْ حَتَّىٰ نَعْلَمَ ٱلْمُجَاهِدِينَ مِنكُمْ وَٱلصَّابِرِينَ وَنَبْلُوَاْ أَخْبَارَكُمْ 

Talal Itani:

We will certainly test you, until We know those among you who strive, and those who are steadfast, and We will test your reactions. Those who disbelieve, and hinder from the path of God, and oppose the Messenger after guidance has become clear to them—they will not hurt God in the least, but He will nullify their deeds.
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Verse 64:12

وَأَطِيعُواْ ٱللَّهَ وَأَطِيعُواْ ٱلرَّسُولَ فَإِن تَولَّيْتُمْ فَإِنَّمَا عَلَىٰ رَسُولِنَا ٱلْبَلاَغُ ٱلْمُبِينُ

So, “Obey God and obey the Messenger.” But if you turn away—it is only incumbent on Our Messenger to deliver the clear message.

Context of the above verse:

64 : 5-11

 أْتِكُمْ نَبَأُ الَّذِينَ كَفَرُوا مِن قَبْلُ فَذَاقُوا وَبَالَ أَمْرِهِمْ وَلَهُمْ عَذَابٌ أَلِيمٌذَٰلِكَ بِأَنَّهُ كَانَت تَّأْتِيهِمْ رُسُلُهُم بِالْبَيِّنَاتِ فَقَالُوا أَبَشَرٌ يَهْدُونَنَا فَكَفَرُوا وَتَوَلَّوا ۚ وَّاسْتَغْنَى اللَّهُ ۚ وَاللَّهُ غَنِيٌّ حَمِيدٌزَعَمَ الَّذِينَ كَفَرُوا أَن لَّن يُبْعَثُوا ۚ قُلْ بَلَىٰ وَرَبِّي لَتُبْعَثُنَّ ثُمَّ لَتُنَبَّؤُنَّ بِمَا عَمِلْتُمْ ۚ وَذَٰلِكَ عَلَى اللَّهِ يَسِيرٌفَآمِنُوا بِاللَّهِ وَرَسُولِهِ وَالنُّورِ الَّذِي أَنزَلْنَا ۚ وَاللَّهُ بِمَا تَعْمَلُونَ خَبِيرٌيَوْمَ يَجْمَعُكُمْ لِيَوْمِ الْجَمْعِ ۖ ذَٰلِكَ يَوْمُ التَّغَابُنِ ۗ وَمَن يُؤْمِن بِاللَّهِ وَيَعْمَلْ صَالِحًا يُكَفِّرْ عَنْهُ سَيِّئَاتِهِ وَيُدْخِلْهُ جَنَّاتٍ تَجْرِي مِن تَحْتِهَا الْأَنْهَارُ خَالِدِينَ فِيهَا أَبَدًا ۚ ذَٰلِكَ الْفَوْزُ الْعَظِيمُوَالَّذِينَ كَفَرُوا وَكَذَّبُوا بِآيَاتِنَا أُولَٰئِكَ أَصْحَابُ النَّارِ خَالِدِينَ فِيهَا ۖ وَبِئْسَ الْمَصِيرُمَا أَصَابَ مِن مُّصِيبَةٍ إِلَّا بِإِذْنِ اللَّهِ ۗ وَمَن يُؤْمِن بِاللَّهِ يَهْدِ قَلْبَهُ ۚ وَاللَّهُ بِكُلِّ شَيْءٍ عَلِيمٌ

Talal Itani:

Has the news not reached you, of those who disbelieved before? They tasted the ill consequences of their conduct, and a painful torment awaits them. That is because their messengers came to them with clear explanations, but they said, “Are human beings going to guide us?” So they disbelieved and turned away. But God is in no need. God is Independent and Praiseworthy. Those who disbelieve claim that they will not be resurrected. Say, “Yes indeed, by my Lord, you will be resurrected; then you will be informed of everything you did; and that is easy for God.” So believe in God and His Messenger, and the Light which We sent down. God is Aware of everything you do. The Day when He gathers you for the Day of Gathering—that is the Day of Mutual Exchange. Whoever believes in God and acts with integrity, He will remit his misdeeds, and will admit him into gardens beneath which rivers flow, to dwell therein forever. That is the supreme achievement. But as for those who disbelieve and denounce Our revelations—these are the inmates of the Fire, dwelling therein forever; and what a miserable fate! No disaster occurs except by God’s leave. Whoever believes in God, He guides his heart. God is Aware of everything.
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These verses, everywhere God ask or command us to obey the messenger, never mentioned of prophets instead of the messengers. We should think/ponder, why messenger not prophets? We see that God wants us to focus only towards the message not on the persons who brought the message. (Quran 5:99 The Messenger’s sole duty is to convey. God knows what you reveal and what you conceal.) These above context of command of “Obey God and obey the Messenger” verifies that we all have to follow/obey only Quran and nothing else;

These are context of the famous verse “Obey God and obey the Messenger” . These above stated context is merely my understanding, and I am open to any logical unbiased explanation of these verses, I know our knowledge is limited and has shortcomings; and our GOD knows the best, who is almighty all-knowing.

May God bless us all.