What is the name of the protagonist of the Metroid series?

The protagonist of the Metroid series is Samus Aran.

Samus first appeared in the original Metroid, released for the Nintendo Entertainment System in 1986. She is a human bounty hunter who was raised by the birdlike Chozo after Space Pirates attacked her home colony and killed her parents. The Chozo infused her with their DNA and trained her as a warrior.

Samus is usually recognized by her Power Suit, an advanced armored exoskeleton equipped with an Arm Cannon, missiles, and other abilities gained throughout her missions. Across the series, she battles Space Pirates, the parasitic X, Metroids, and recurring enemies such as Ridley and Mother Brain.

A famous twist in the first game revealed that the armored hero was a woman; the instruction manual had used male pronouns to preserve the surprise. Samus is sometimes mixed up with Master Chief, but Master Chief belongs to Microsoft's Halo series, while Samus is Nintendo's central Metroid hero.