Super Unit is one of the two rewards you can choose after you have upgraded a level 4 city to level 5 and then after every subsequent level (the other being Park). It spawns in a Giant, which can also be obtained from ruins. If you are playing as the Aquarion, a Crab is spawned instead of a Giant.
Some notable advantages to choosing this upgrade are that it gives you an end-game unit, but can also be used tactically. If an enemy unit is capturing your city, the unit will be displaced out of your city if you spawn in a Super Unit.