The Mega Man Zero series stars Zero, waking up from hibernation far in the future (Meaning past the Mega Man X series), fighting alongside a resistance group led by Ciel. This group is resisting Neo Arcadia, an oppressive rule that exterminates reploids. This rule is led by none other than Mega Man X. It is later revealed by the first game that this is not the true X, but a copy. The true X has been helping Zero by giving him back his Z-sabre in the beginning of the game. He has grown tired of the battles and the fighting and now wishes to rest, while Zero takes up the burden of fighting the remains of Neo Arcadia.
The games in the series are all 2D platformers. Your standard Mega Man fare, except with more emphasis on melee combat, and Pokémon-like Cyber Elves that give you certain power-ups, abilities, or helping hands throughout the level. The series is, so far, exclusive to the Game Boy Advance. They are also notoriously difficult, some even being considered unfairly cheap.