He offers all the obligatory prayers in the mosque except for Fajr. What is the ruling on that?

You should note that Allah has blessed you by enabling you to offer the prayers in the mosque with the congregation, to stand before Allah in His house and establish this great ritual of Islam and to do that which Allah has enjoined upon you. There is nothing that is more beloved to Allah than fulfilment of what He has enjoined. We have already discussed the obligation of praying in congregation in question no. 8918. 

With regard to what you say about praying Fajr in your house, this is a sin for which you must repent to Allah, and it is a problem from which you are suffering and we ask Allah to help you to overcome it. That is because the evidence which indicates that it is obligatory to pray in congregation does not apply only to some prayers and not others, rather it is general in meaning and applies to all the prayers, the first of which is Fajr, about which you are asking. 

How can you feel comfortable about not praying Fajr in congregation and depriving yourself of complete light on the Day of Resurrection? Abu Dawood (561), al-Tirmidhi (223) and Ibn Maajah (781) narrated from Buraydah (may Allah be pleased with him) that the Prophet (peace and blessings of Allah be upon him) said: “Give glad tidings to those who walk to the mosques in the dark, of perfect light on the Day of Resurrection.” Classed as saheeh by al-Albani in Saheeh al-Targheeb. 

How can you feel comfortable about not praying Fajr in congregation and depriving yourself of meeting the angels and their testifying for you before your Lord? Al-Bukhaari (555) and Muslim (632) narrated from Abu Hurayrah (may Allah be pleased with him) that the Messenger of Allah (peace and blessings of Allah be upon him) said: “Angels come to you in succession, night and day, and they meet at Fajr prayer and ‘Asr prayer, then those who stayed among you overnight ascend and [Allah] asks them – although He knows better about them – ‘How did you leave My slaves?’ and they say, ‘We left them when they were praying and we came to them when they were praying.’” 

How can you feel comfortable about not praying Fajr in congregation and depriving yourself of the reward of spending half the night in prayer? Muslim narrated in his Saheeh (656) that ‘Uthmaan (may Allah be pleased with him) said: I heard the Messenger of Allah (peace and blessings of Allah be upon him) say: “Whoever prays ‘Isha’ in congregation, it is as if he spent half the night in prayer, and whoever prays Fajr in congregation, it is as if he spent the whole night in prayer.” 

According to a report narrated by Abu Dawood (555) and al-Tirmidhi (221): “Whoever prays ‘Isha’ in congregation, it is as if he spent half the night in prayer, and whoever prays ‘Isha’ and Fajr in congregation, it is as if he spent the (whole) night in prayer.” 

How can you feel comfortable about not praying Fajr in congregation and depriving yourself of the protection of Allah? It was narrated that Abu Bakrah (may Allah be pleased with him) said: The Messenger of Allah (peace and blessings of Allah be upon him) said: “Whoever prays Fajr with the congregation will be under the protection of Allah, and whoever violates this protection of Allah, Allah will throw him into the Fire on his face.” Al-Haythami said in Majma’ al-Zawaa’id: This was narrated by al-Tabaraani in al-Kabeer in a hadeeth; this is its wording and its men are the men of saheeh; it was also classed as saheeh by al-Albani in Saheeh al-Targheeb. 

The origin of this hadeeth is in Saheeh Muslim, in the chapter entitled The virtue of praying ‘Isha’ and Fajr in congregation (657). “Whoever violates the protection of Allah,” means by harming and offending the believer who prayed Fajr in congregation. 

How can you feel comfortable about not praying Fajr in congregation when the Prophet (peace and blessings of Allah be upon him) has told us that feeling that it is too burdensome to pray Fajr in congregation is the sign of the hypocrites? Al-Bukhaari (657) and Muslim (651) narrated that Abu Hurayrah (may Allah be pleased with him) said: The Messenger of Allah (peace and blessings of Allah be upon him) said: “The most burdensome of prayers for the hypocrites are ‘Isha’ and Fajr. If only they knew what (reward) there is in them, they would come to them even if they had to crawl. I was thinking of ordering that the call to prayer be given, then I would tell a man to lead the people in prayer, then I would set out with some men carrying bundles of wood and go to people who do not attend the prayer, and burn their houses down with them inside.” 

‘Abd-Allah ibn ‘Umar (may Allah be pleased with him) said: “When we noticed that a man was not present at Fajr and ‘Isha’ prayer, we would think badly of him.” Narrated by al-Haakim in al-Mustadrak, 764, and elsewhere; he classed it as saheeh according to the conditions of the two shaykhs (al-Bukhari and Muslim), and al-Dhahabi and al-Albani agreed with him. 

The Muslim who is keen to attend the prayers in congregation, as you describe yourself, would not feel comfortable, in sha Allah, to miss praying Fajr in congregation, after hearing what the Prophet (peace and blessings of Allah be upon him) said about that. 

May Allah help us and you to do that which He loves and which pleases Him.