Assalamualaikum! Praise be to Allah (swt). Please provide guideline in the following scenario- A person goes to the Masjid in Fajr and finds that the Salat has already started. Should he say the Sunnat prayer first and then join the congregation even if it means that he may miss the congregation or should he skip the 2 units of Sunnat and join the congregation immediately. Jazakamullah Khairan
Praise be to Allaah.
The person should join the congregation right away. He can perform the 2 rakats of (missed) Sunnah Prayer of Fajr EITHER immediately after the congregational (Fard) prayer OR he may wait till the sun comes up completely (roughly about half an hour after the official sunrise time).
Also please see the following from Islam Q-A:
[Source: http://www.islam-qa.com/en/ref/39 ]
If a person enters the mosque and is praying the sunnah while the iqamah is called, then the best opinion in this case is that if he is in his second rak‘ah, he should shorten it, and if he is in the first rak‘ah, he should just break his prayer and enter the congregation with the Imam. The evidence for this comes from what Imam Muslim has narrated in his Sahih:
Prophet (peace be upon him) said: If iqamah is called for the prayer then there is no prayer except the obligatory one. (Sahih Muslim, 1/493)
So, if one has performed the ruku‘ for the second rak‘ah, then he should complete the prayer, and if not, then he should discontinue because what is left from his sujud and tashahhud is not needed any more. Moreover, he should break without salaam, and it is enough to have the intention in the heart, contrary to common misconception.
Fatawa Ibn ‘Uthaymeen, 1/345