Can You Make Up Missed Prayer in Congregation?
Question

Should missed prayers be made up individually or in congregation? We went out in the countryside one day and we did not wake up for Fajr prayer. After the sun had risen, we made up the prayer, praying individually, because the time for the prayer had ended. Is what we did correct?
Praise be to Allah.It is prescribed to pray in congregation when making up missed prayers , because of the report narrated by Al-Bukhari (595), Muslim (681) and An-Nasa’i (846) from Abu Qatadah (may Allah be pleased with him) who said: We were with the Messenger of Allah (peace and blessings of Allah be upon him) (on a journey) and some of the people said: Why don’t you let us stop to rest (at the end of the night) O Messenger of Allah? He said: “I am afraid that you will sleep and miss the prayer.” Bilal said: I will keep watch for you. So they lay down and went to sleep, and Bilal leaned back against his mount. The Messenger of Allah (peace and blessings of Allah be upon him) woke up and saw that the edge of the sun’s disk had risen. He said: O Bilal, what about what you said? He said: I have never slept like that. The Messenger of Allah (peace and blessings of Allah be upon him) said: “Allah took your souls when He willed and He returned them when He willed. Get up, O Bilal, and call the people to prayer.” So Bilal got up and called the people to prayer, and they did Wudu, i.e., when the sun had gotten high, then he stood up and led them in prayer. 
Ibn Qudamah (may Allah have mercy on him) said in Al-Mughni (1/356): “It is recommended to make up missed prayers in congregation . In the battle of Al-Khandaq, the Prophet (peace and blessings of Allah be upon him) missed four prayers, and he made them up in congregation. And in the Hadith of Abu Qatadah and elsewhere it says that when the Prophet made up for Fajr prayer on the day of Al-Khandaq, he and his companions, he led them in offering the prayer in congregation.”
Shaykh Ibn ‘Uthaymeen (may Allah have mercy on him) said: From the hadith of Abu Qatadah (may Allah be pleased with him) it may also be understood that it is prescribed to offer made-up prayers in congregation if there is a group, because making up is to be done as one would have performed the prayer. If they would have offered the prayer in congregation if they had prayed on time, then when they make it up they should offer it in congregation. This is also mentioned in the Sunnah in the Hadith of Abu Hurayrah (may Allah be pleased with him), when the Messenger (peace and blessings of Allah be upon him) told Bilal (may Allah be pleased with him) to give the call to prayer, then he prayed two (Sunnah) Rak`ahs of Fajr, then he led them in praying Fajr prayer in congregation.” (Al-Sharh Al-Mumti’, 2/140)
Based on this, it would have been better for you to give the call to prayer and offer the Sunnah prayers individually, then recite the Iqamah and offer the prayer in congregation, as the Prophet (peace and blessings of Allah be upon him) did with his companions. 
For more about prayer in congregation, see these answers: 40113 , 79 , 8918 , and 52906 .
And Allah knows best.