Emperor Aurangzeb requested Hadhrat Khwaja Masoom Naqshbandi (May Allah shower His mercy on him) to send one of his caliphs for his own guidance. Khwaja Masoom (May Allah shower His mercy on him) gave this responsibility to his own son, Hadhrat Khwaja Saifuddin Naqshbandi (May Allah shower His mercy on him). Enjoining the good and forbidding evil was second nature to Hadhrat Saifuddin (May Allah shower His mercy on him). He was very strict in imposing the laws of the Shariah and in deterring innovations in religion.
On his insistence, music and singing were stopped in the royal court. Singers and musicians are anyhow playful. They thought of a plan that they carried a bier before the emperor’s escort and cried and wailed a lot. The emperor inquired whose bier it was. They replied that it was the bier of music. The emperor was also very witty. He replied: Bury it deeply so that it can’t come out again.
Once the emperor took the Shaykh to Hayaatbaksh Garden. There, sculptures fishes of gold with rubies and emeralds as their eyes were there. The Shaykh said: Until these are not done away with, I will not sit here. The royal servants were hesitating in breaking them as they were made of gold, but the emperor ordered them to be broken and said that the pleasure and approval of the Shaykh is more beneficial.
The Shaykh would be seated on a chair in the royal court and nobles would respectfully stand around him. A saint says: I got the thought that this is a dervish and he was so much pride. The next moment, the Shaykh turned to me and said: Our pride is through the majesty of the Lord Almighty.
In spite of all this, the Shaykh was very humble. Often he would address himself as a dog of Hadhrat Mujaddid Alh Thaani (May Allah sanctify his secret)
Once the Shaykh was on a platform making his ablutions for Tahajjud. Suddenly, sound of Sama’a (religious music) reached him. He went into ecstasy on hearing it and fell down from the platform. He received an injury on his blessed hand due to the fall. When he regained consciousness in the morning, he said: The people of Sama’a think that we are without emotions although on listening to Sama’a once, my condition became so that I though my relation with life will be snapped. How can those people who listen to Sama’a bear it? In the interests of justice, who is emotionless, us or them? They are unaware of our hidden emotions. We are calm like ash on the outside, but our inward aspects are aflame with sorrow and yearning. Our order is like that of Hadhrat Abu Bakr Siddiq (May Allah be well pleased with him) who was very calm and composed on the outside, but the sighs escaping from his heart had blackened the roof of his house.
Once a disciple of the Shaykh was going from Kabul to his own land. Before him, a Raafdhi was traveling. That man insulted Hadhrat Abu Bakr and Hadhrat ‘Umar (May Allah be well pleased with them). This disciple got angry, drew his sword and beheaded him. Later, he became fearful that the friends and relations of that man will hurt him. Suddenly, a masked man appeared and told him: Don’t worry! I have turned him into a donkey. The disciple turned and saw that indeed the deceased had been turned into a donkey.
The disciple requested the masked man to let him see his face. The masked man removed his mask and he was Khwaja Saifuddin Naqshbandi (May Allah shower His mercy on him) himself.
A person suffering from leprosy was brought to the Shaykh. The Shaykh blew on him and he was instantly cured.
His elder brother, Hadhrat Hujjatullah Muhammad Naqshbandi (May Allah shower His mercy on him) was going for Hajj. He told the Shaykh: I have reached a great age. Take care of my children. The Shaykh said: I have hopes that your age will be even greater. However, I have no hopes for myself. Thus, you should take care of my children. This is what happened. Before Hadhrat Hujjatullah (May Allah shower His mercy on him) returned from Hajj, Hadhrat Saifuddin (May Allah shower His mercy on him) passed away and he lived on for 19 more years.
The Shaykh had a custom that between Zuhr and ‘Asr, he would give a lesson on Hadith for women. Once he finished the lesson very early. When requested that there was still a lot of time and the lesson be continued, he said: Muhammad Azam will teach the rest. Khwaja Muhammad Azam (May Allah shower His mercy on him) was his eldest son. After this, the Shaykh fell ill and couldn’t give any lessons of Hadith.
Before his demise, a doctor was brought whose beliefs were not per the Ahle Sunnah. On seeing him the Shaykh said: What time is this to bring me a man of the wrong beliefs? Send him away! Thus, that man was sent away.
After passing away, the Shaykh was buried in the south of the mausoleum of Hadhrat Imam Rabbani Mujaddid Alf Thaani (May Allah sanctify his secret).
The Shaykh had 8 sons. The eldest being Khwaja Muhammad Azam (May Allah shower His mercy on him), a master of the normative and mystical sciences and an author of many books.