Shaikh Ibn ul-‘Uthaymeen rahimahullah was asked:
A man missed the fajr prayer with the congregation. Does he pray the Raatibah [the Sunnah] or the obligation knowing that the congregation has left?
He precedes the Raatibah over the obligation because the Sunnah of fajr is before the obligation. (This is the case) even if the congregants have left the Masjid
[Majmoo’ al-Fatawa wa Rasaail question no. 868]
Faisal Ibn Abdul Qaadir Ibn Hassan