When joining the congregation late, how should prayer be made up afterwards?

When the Imam completes his prayer, the person who joined the prayer late should stand up saying Allahu-Akbar rather than saying salam. He should observe his remaining prayer as though he is observing the prayer from the beginning by himself, meaning that he should start the first rak‘at with thana and a‘uz, and after Fatihah he should recite another chapter as well. If he has to observe the second rak‘at as well, then he should recite a chapter other than Fatihah in it. However, if he only observed one rak‘at with the Imam, then he has this option that after the first rak‘at he can sit for the middle qa’dah, or after observing two rak‘at he can sit for qa’dah. Any option from these two options can be adopted (Fiqh Ahmadiyya, vol. 1 p. 127).

Also, Hadrat Khalifatul-Masih IV ^rta explained that we should only stand up to make up our prayer after the Imam has finished saying the second salam, not before (Question Answer Session, Aug 23, 1984).