If someone intentionally missed Fajr prayer and then repented, must he make up the prayers that followed it in their proper sequence, or only Fajr? And what if this recurred for years?

A missed Fajr prayer must be made up immediately at any time, whether it was missed intentionally or due to forgetfulness. The worshiper does not need to repeat the prayers he performed on time. If more than one prayer was missed, then these missed prayers should be performed in their proper sequence.