Ash-Shaykh al-Uthaymeen was asked the following question,
Question: 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?
Answer: “He precedes the Raatibah over the obligation because the Sunnah of fajr is before the obligation. Even if the congregants have left the Masjid”
[Majmoo’ al-Fatawa wa Rasaail question no. 868]
Faisal Ibn Abdul Qaadir Ibn Hassan