Plot

In this remake of "Metroid (1986)", the full story of Samus Aran's first mission unfolds: After having defeated Mother Brain, Samus crashes on Zebes and has to face a trial in the ruins of Chozodia that explore her past.

Some background from the game instruction manual: In the year 20X5, a Galactic Federation deep-space research ship landed on the planet SR-388 on a routine survey. The crew discovered dangerous organism, dubbed Metroids: a species of vicious jellyfish-like predators that can absorb the life energy from a living prey without draining it of their blood or other vital fluids. When unleashed, they could potentially eradicate entire planetary populations in a short time. The scientists took several Metroid specimens in suspended animation with them and returned toward the Federation Headquarters, but underway, they were ambushed by a group of Space Pirates: nomadic criminals who only desire wealth and power for themselves. The Pirates took the Metroids to planet Zebes for further study. They were experimental in nature and regarded the Metroids as little more than guinea pigs, their means to Galactic domination. The arrogant fiends did not seem to realize that Metroids were far too dangerous to be kept imprisoned. The parasites had to be prevented from escaping, or else they could endanger all life in the Galaxy. The Galactic Federation tried to take back Zebes several times, but the Space Pirates defences were simply too strong.

The in-game story: Bounty hunter Samus Aran was selected by the Galactic Federation for a mission of vital importance: to infiltrate the planet Zebes, defeat the invading Space Pirates and the mechanical life-form, Mother Brain, and exterminate all Metroid organisms.

The story of her heroic conquest became widely known throughout the Galaxy. But it was not until years after the mission that Samus told the entire story: "Planet Zebes.... I called this place home once, in peaceful times, long before evil haunted the caverns below. Now, I shall finally tell the tale of my first battle here... My so-called Zero Mission":

Samus successfully made an undetected landing on Zebes with her Hunter-class ship. She beamed down into the vast system of subterranean caverns. Once a familiar place where she grew up with her guardians, the Chozo; now defiled by the evil Space Pirates and infested with traps and dangerous creatures. Samus, however, was no ordinary soldier; she wore a special Chozo power suit which acts as armor, and was also equipped with an arm cannon. There were several larger areas that made up Zebes and the underground dwellings. The surface area was called Crateria, and it still housed many of the ancient ruines built by the Chozo. Brinstar and Norfair were the upper subterranean levels, comprised of long horizontal and vertical caves. During her initial exploration of these areas, Samus found a strange 'door' which consisted of two stone heads; they represented Kraid and Ridley, two of the Space Pirates' high-ranking members. It was clear that access through this doorway would only be possble upon the defeat of these two enemies. Samus also found old chambers still preserved, where the Chozo had left statues with powerful weapons and upgrades for her Power Suit, which dramatically increased her already impressive combat power. One of the more unique additions to her suit was the ability to roll up into a metal ball, in order to access very small spaces. However, there were also several unknown items which her suit could not identify, but they did give her access to more types of doors. The upgrades proved to be essential to gain access to the deeper areas, Kraid and Ridley, which were even more dangerous and treacherous. The Kraid area was named for the gigantic high-ranking dinosaur-like monstrosity of the same name, whom Samus encountered. However, size did not matter, as he was big and sluggish, and ultimately no match for Samus' fighting skills and weapons. Still deeper into the complex, she entered the Ridley area, where she was finally standing face-to-face with the evil Ridley, the pterodactyl-like military leader of the Space Pirates; the fiend was once personally responsible for killing Samus' mother. The ensuing battle was fierce bcause Ridley was much more manoeverable, but Samus emerged victoriously. There were two final obstacles left: the Metroids, and the entity that ran the entire Pirate operation: Mother Brain.

Upgraded to full power, the Tourian area, which served as the Space Pirates' laboratory and control center, had finally opened upon the death of Kraid and Ridley. As soon as she got in, she encountered the Metroids: the creatures had already escaped from their confinements, and killed many Space Pirates by sucking them dry of their body energy. But, by a happy coincidence, Samus suit had already assimilated an Ice Beam; a susceptibility to cold temperatures appeared to be one of the Metroids' few weaknesses. Freezing them and then blowing them up with missiles was a very effective means of destroying them. Fighting her way through the Metroid horde, Samus finally reached the heavily defended laboratory. Laser turrets, acidic floors and regenerating walls protected the Mother Brain at the end of the hall: an eerie one-eyed brain inside a fluid-filled jar. It took Samus most of the missiles that she collected underway to blast the hideous thing into oblivion, but unfortunately, Mother Brain was connected to the entire base's defence system: its demise immediately activated the base's self-destruction system, giving Samus only a few minutes to escape. Samus quickly worked her way through a long vertical escape shaft to the surface, boarded her ship and flew away safely, to see the surface of the planet light up by a massive explosion. Reassured that she had fulfilled her mission, Samus unwisely took off her Power Suit. However, this momentary lapse in concentration allowed several Space Pirate shuttles still flying around Zebes to surround her. Samus tried to make a quick escape, but could not prevent the Pirates from shooting down her ship. She succeeded in getting out before her ship got smashed into the planet's surface. In the distance, the Space Pirate Mother Ship had landed: "The timing of my escape couldn't have been worse. I was attacked by Space Pirates and left nearly defenseless, stripped of my Power Suit. All I had for protection was my rather useless emergency pistol. Infiltrating the Space Pirate Mother Ship so armed may have been foolish, but I had no choice... Could I survive long enough to escape?"

Samus infiltrated the ship, but she was seen by a detector, so the Pirates were on the look-out for here. Through stealth action and several quick escapes (upon detection by the Pirates), she made her way through the ship and found out that it had landed next to a very ancient Chozo temple, an area called Chozodia. The temple grounds were also infested with Pirates, and she finally arrived in an old shrine. Samus remembered going there once with one of her Chozo mentors, a long time ago. There was a picture of a Chozo elder wearing a Power Suit in the room, which sprang to life and started to attack Samus. However, even with a mere emergency gun, Samus' impressive display of fighting skills made it recognize her as the Warrior, and revealed a brand new, fully armed Power Suit. The unknown items she had picked up earlier were finally identified and fully employed, upgrading the suit to full power, so it could even withstand the heat of lava. The shrine was sealed off forever when she left it. Samus fought her way through the Pirate ship's shuttle bay, but she suddenly got trapped inside a room together with a mechanical version of Ridley! The new Power Suit enabled her to defeat her nemesis once again, but the dying fiend also activated its self-destruct system. Samus rushed to the shuttle bay, commandeered a Pirate shuttle, and flew out into open space. She witnessed the explosion of the Mother Ship from space. The mission was accomplished and Samus had taken her revenge.. for now.

A final look in the Chozodia shrine reveals a small drawing made by young Samus: her depiction of herself and two of her Chozo guardians.