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There are two possible options for the retireval of the Mako after a mission. One is that the Normandy simply lands and the Mako drives on board, muck like on Virmire. The other is that the Mako uses it's element zero drive core to to lighten its weight and fires it thrusters to reach an airborne Normandy.

Edit 1: The second option is much more likely, considering it is very dangerous for a space vessel to enter the atmosphere. Gravity may become too great for it, or elements in the atmosphere could begin a chain reaction.