The masjid of the Prophet Muhammad (s) was built in Medina before his death (before his grave). His house was right next to the masjid and he said, "Each prophet is to be buried where he died". He died in the room of his wife Aisha (next to the masjid) and so he was buried there. This room had only enough space for four graves, so the companions Abu Bakr and Omar were also buried in the graves next to his. The fourth space is said to be where Isa (a) will be buried when he dies after he returns to Earth, Wallahu ‘aalam .
According to hadith, the Prophet (s) prayed to Allah that his grave does not become a shrine for people. Alhamdulilah, he was never worshipped throughout history by anyone because Allah did not ever allow anyone to do so. During the Prophet's (s) time, the masjid was very small, but during the time of Omar and Uthman, there were extensions added to the masjid and the grave of the Prophet (s) was never actually in the masjid. During the khilafah of Alwaleed ibn AbdulMalik, the extensions continued and it looked as if the grave was in the masjid, but it was at the end of the masjid, not in the front where people pray. Extentions will always be added on, but on the north and west wings of the masjid (south is the direction of the kibla, east is the direction of the grave) leaving no opportunity for the grave to ever be inside the masjid. Throughout history, the extensions continued away from the grave and it is still done this way. The height of the grave of the prophet and his companions with him was no more than a foot tall and were made from mud, as taught by him .
During the 12th century, Sultan Nordeen Mahmood bin Al Zinkee of Aleppo (Halab), who was the father-in-law of Salahuddin Al Ayoubi, had a dream about Prophet Muhammad (s) continuously for three nights. In the dream, Prophet Muhammad showed Nordeen two blonde men and said that they were trying to harm him. Nordeen asked his advisor about his dream and they advised him to go to Madina .
Nordeen informed all the poor people of Madinah to meet him in order to discuss their problems and give them gifts. Upon their gathering, he asked if everyone in Madina had come and they told him that two old men did not attend. Nordeen then went to their house and recognized them from his dream. These two men were from Al-Andalous (Spain) and said that they were in Madinah to worship. Nordeen did not believe them and had them interrogated. They admitted that they were digging a tunnel to damage Prophet Muhammad’s body, and they found under a mat a tunnel that extended to the left foot of Umar, and they found that there was a body there, not a skeleton. Nordeen had the two men killed. He then ordered molten lead to be filled all around the grave to protect the body of Prophet Muhammad (s). The successful khalifas, Abu Bakr and Omar bin Al-Khattab were also buried on the left side of the Prophet’s grave. Later, the Turks built the green dome on the grave of Prophet Muhammad .
When the companions opened the current Muslim lands, they did not find any graves of any prophet on their journeys--not Ibrahim, Musa, Isa, Zakariya, Yahya, etc. except during the time of Omar bin Al-Khattab. When the Muslims opened Persia, in the city of Testar, they found a tomb of Prophet Daniel. These Muslims (story narrated by Khalid ibn Sinan), some of them former companions of the Prophet (s), led by Abu Musa Alashari, found the body of Prophet Daniel in the house of Hurmazan (a king of Persia) preserved. It looked like he died fairly recently although according to history he died three hundred years before the arrival of these Muslims. According to Islamic practice, the graves can only be a foot tall, and because the tomb was very tall and high, they sent a letter to Omar for advice about what to do in this situation. He replied by saying that they should dig thirteen graves during the day and put his body in one of them at night and to keep secret about which grave he is in so that no one would ever worship it .
As narrated by Abu ‘Aaliyah ibn Yunis ibn Bakir, the Prophet (s) said, “Daniel said, ‘ The umma of Muhammad will bury me.’” The Prophet (s) spoke about Prophet Daniel because it was the only grave to exist and not only that, but reinforces the proper way to bury a body particularly of a prophet. This hadith proves the khilafah of Omar and the righteousness and legitimacy of the sahabah. It is also evidence of the prophecies of Muhammad that have been fulfilled .
These Muslims then went to Mosul and did not find the grave of Yunus or any other prophet, they also went to Palestine and did not find the graves of Musa, Ibrahim, etc. They did not find any prophet’s grave in any Arab region, and even throughout history, the predecessors, Christians, Jews, followers of Yahya, etc. did not make any graves for these prophets because there was no one to do it. Only Jews made the tomb of Daniel and showed it to the Muslims when they arrived and explained it as his grave so that Muslims would not destroy it. All the other graves of any other prophet is false .
For example, Allah did not allow for Isa to be killed and buried, so his grave would not be worshipped, and instead raised him to heaven and this is what Muslims believe. According to Jewish history, Musa told his followers that he was about to die and must leave him alone because Allah would take care of him, and went alone somewhere and died as mentioned in the Torah Deter. 34.. As for the graves of the companions of the cave, they are said to be in Jordan, others say in Syria or Turkey, and fourty-four different cities in Turkey say it is in their city. The murderer, Abu Luluah Fayrouz Al-Majusi, of Omar was buried in Madinah, yet there is a tomb for him in Iran for worship (pay respects), and Hussein, the grandson of the Prophet (s), Iraq, Syria, and Egypt all claim his grave is there. This situation is the same for many other famous righteous people .
The best advice about deciding to remove the graves must come from government officials, and these officials must be advised by religious scholars, who then have to teach people about the matter before they make these decisions and until they find people well educated on the matter. If there is any grave inside a masjid, in order to respect it, the grave and corpse/skeleton must be removed at night and taken to the Muslim cemetery to be buried anonymously. If there is a grave with no corpse inside, then the grave must be removed without destroying the masjid, since it is already in use as a place to worship Allah and destroying would cause fitnah. Lastly, everyone must be straight with Allah, worship him alone, please him alone, and follow His teachings and the teaching of his Prophet (s ).
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