Samus travels through the caverns of the planet Zebes to stop the Space Pirates from exploiting the parasitic organisms known as Metroids for galactic domination. She confronts the cybernetic lifeform Mother Brain, as well as its guardians, Kraid and Ridley. It was released on the Nintendo Entertain- ment System, also known as the NES.
The Galactic Federation deems the Metroid species too dangerous to exist, and after their own failed attempts, employs Samus to travel to the Metroid homeworld, SR388, and exterminate the entire species. After kill- ing every Metroid (among them Alpha, Gamma, Zeta, and Omega Metroids) and the Queen Metroid, Samus finds an unhatched egg behind the Queen Metroid's chamber. Before Samus fires on the Metroid egg, an infant Metroid hatches and believes Samus to be its mother. After it helps her escape back to her ship, Samus hands the hatchling over to the Ceres research station for study. It was released on the Game Boy, and is also available on the 3DS Virtual Console.
Just after she leaves, Samus receives a distress signal from the Ceres re- search lab. She returns just in time to catch Ridley stealing the hatchling, having killed all of the scientists. She follows Ridley to a rebuilt base on Zebes, where the Space Pirates are once again attempting to clone the Metroids and use them as weapons. Samus kills the reborn versions of Ridley and Kraid, as well as new guardians Phantoon and Draygon, then confronts Mother Brain once again. Samus is nearly killed in the battle, but the Metroid hatchling, now having grown immensely, rescues her. Mother Brain kills it just after it restores Samus's energy, and Samus in turn destroys Mother Brain with a supercharged weapon known as the Hyper Beam apparently left by the hatchling's death. She then escapes Zebes during a countdown that leads to the entire planet exploding, taking with it the few remaining cloned Metroids. It was released on the Super Nintendo Entertainment System (SNES), and said to be "one of the greatest games of all time" by IGN.
While acting as a bodyguard for researchers on the planet SR388, Samus is infected by a native creature known as the X Parasite, originally the prey of the Metroid species. Doctors surgically remove portions of her armor and cure the X infection with a vac- cine created from the DNA of the Metroid hatchling (Metroid II: Return of Samus). The vaccine not only allows her to survive the parasites, but to absorb them to power up her energy and weap- ons. She is then sent to investigate a disturbance at the Biologic Space Labs research station, where it is revealed that specimens from SR388 had been carriers of the X parasite. An X mimicking Samus, nicknamed the SA-X, has taken control of Samus's old suit, methodically breaking into different parts of the station to allow the X parasites to infect the entire station. While trying to destroy the rapidly multiplying X as well as clones of the SA-X, Samus dis- covers a secret Federation Metroid breeding program. Before Samus can react, the SA-X discovers the lab and triggers a security system that ejects it into space, killing the Metroids (as the X Para- site and Metroid are natural enemies). The Federation eventually shifts interest towards researching the X parasite, especially the SA-X's capabilities, and orders the shipboard computer to prevent Samus from destroying it. Samus then convinces the computer, whom she had nicknamed "Adam" after her former Commanding Officer, that the X pose a threat to galactic civilization, claiming that the arriving Federation troops will be overwhelmed by the multiple SA-X patrolling the ship. Adam, in a sudden change of heart, sug- gests that she alter the station's propulsion to intercept with SR388 to destroy the planet and wipe out both X populations. After fight- ing one of the SA-X clones and changing the station's propulsion, Samus races back to her ship, where she encounters an Omega Metroid which seems to have escaped the laboratory breach. The SA-X returns and tries to kill the Metroid, since the ice-beam it has seems to be the only weapon able to damage it, but the SA-X is badly damaged in the battle. Samus absorbs the SA-X parasite to regain her suit's Energy, defeats the Omega Metroid and leaves the station before it collides with SR388. It was released on the Game Boy Advance.
Samus receives a distress signal in her new ship and travels to Tallon IV to stop the Space Pirates from exploiting a powerful radioactive substance known as Phazon. She discovers that the Chozo once set- tled on this planet, and their disappearance, as well as the emergence of Phazon, is due to a meteor impacting the planet decades ago. After ruining a Space Pirate mining operation and collecting the twelve Chozo Artifacts that allow access to the sealed impact crater, she con- fronts and defeats Ridley before delving deeper into the impact site and discovering Metroid Prime, a matured Metroid, mutated and cor- rupted by Phazon. Metroid Prime had been feeding off the Phazon Core of the meteor to increase in size and strength. During the final battle against Metroid Prime, Metroid Prime grabs and takes Samus's Phazon Suit from her. She flees the impact site and after the credits, there is a glimpse of a dark hand coming out of a pool of Phazon in the arena where Samus and Metroid Prime fought. It is implied that this hand is Dark Samus in the future games and that Metroid Prime by taking Samus's suit becomes Dark Samus. It was released on the GameCube and is the first of the Metroid Prime Trilogy.
Metroid: Zero Mission is an enhanced remake of the original Metroid designed to retell the game's story. It has an addendum to the original storyline: After defeating Mother Brain, Samus is am- bushed by Space Pirates and her ship crash-lands back on the surface. With her ship and arsenal destroyed and armed with only an emer- gency pistol, she is forced to infiltrate the Space Pirate mothership to find a way off the planet. She finds ancient Chozo armor more power- ful than her original while deep within Chozo ruins, then goes on to defeat the Ridley Robot and escapes from the mothership before it self-destructs. It was originally released on the Game Boy Advance, and a version was released for the Wii U Virtual Console.
Samus is sent to investigate the planet Aether after a squad of GF Marines was lost there. Samus finds them all dead, killed by several creatures, mostly by an evil race called the Ing. The Ing possess life forms, transforming them into monstrous "dark" versions of their former selves to wage war with Aether's dominant race, the Lumi- noth. Upon meeting the only remaining member of Luminoth (the others are frozen in stasis chambers, awaiting the destruction of the Ing), Samus learns Aether has been split into two dimensions by a meteor similar to the one that crashed on Tallon IV. Samus agrees to assist by recovering Aether's planetary energy (the "Light of Aether") from Dark Aether. She does this by going to Dark Aether and absorb- ing the energy into her suit, then placing the energy back into the Energy Controllers on Light Aether. By completing this task, she de- stroys Dark Aether and the Ing that inhabit it. The final boss fights consist of one against the Emperor Ing and Dark Samus. Dark Samus vaporizes in front of Samus's eyes, but as she flees, Dark Samus is shown to reform in outer space. It was released on the GameCube in 2004.
Metroid Prime Pinball is a pinball version of Metroid Prime, following the same storyline and has similar gameplay elements; however, it is just presented through pinball format rather than as a first-person adventure.
When the Federation receives an unusual telepathic message re- garding an "Ultimate Power," Samus is sent to the remote Alimbic Cluster in the Tetra Galaxy to investigate and secure it. Others have also received the message, and six rival bounty hunters arrive with similar intent. When all parties arrive at the source of the transmission, it is revealed that the message was a false lure sent by an ancient creature known as Gorea, who intended to manipulate visitors into re- leasing it from a void between dimensions. Upon this revelation, Gorea attacks and syphons the energy from the other hunters, allow- ing it to commandeer their weapons. After killing Gorea, Samus and the other hunters escape the cluster, empty handed, but alive. It was released on the handheld Nintendo DS in 2006. It was also the first game that many played on the DS since, at its original release in some regions, the console came bundled with a demo, Metroid Prime Hunt- ers: First Hunt.
Samus, along with bounty hunters Rundas, Ghor, and Gandrayda, are brought together in a ship over Norion to discuss a Space Pirate infection sweeping the Galactic Federation supercomputer network, one com- posed of organic Aurora Unit systems. Having this network shut down allows for the Pirates to engage in large scale combat in an attempt to fur- ther spread Phazon. As a battle erupts on Norion's surface, enormous Pha- zon-based seedships, called Leviathans, also begin to rain from the sky onto planets in order to begin corrupting them with Phazon. After a skir- mish with Dark Samus which left her asleep for a month, Samus is charged with destroying these "Phazon Seeds" and restoring functionality to the Federation's computer network, as the other three hunters have mysteriously cut all contact during their missions. Samus is told that after the battle on Norion, her body gained the capability to self-generating non-hazardous Phazon, allowing for her to enter a "Hypermode" attack frenzy with her suit's PED (Phazon Enhancement Device). After purging three planets of Phazon (including a Space Pirate homeworld), the Federa- tion locates the source of Phazon - planet Phaaze - which is made entirely of Phazon. As the Federation engages the Space Pirates in orbit, Samus enters the depths of the planet and succeeds in destroying Dark Samus and Phaaze, rendering all Phazon in the galaxy inert and cleansing her body from its corruption. A ship is seen following her into Warp Space at the end. It is the third game of the Metroid Prime series, and was released for the Wii console.
Samus receives a distress signal and follows it to a mysterious vessel named the Bottle Ship. There, she encounters a squad of Galactic Federa- tion soldiers, including her friend Anthony Higgs and her former superior officer Adam Malkovich. They find out that the director of the ship, Made- line Bergman, has been conducting research on illegal bioweapons for the Federation. Eventually, Samus finds a survivor who claims to be Madeline Bergman, but is later revealed to be an android with an artificial intelli- gence duplicating that of Mother Brain, so that the bioweapon Metroids can be telepathically controlled. The Federation soldiers are mysteriously killed by a secret assassin among their ranks. Samus refers to this assassin as "the Deleter". His or her identity is never explicitly revealed in-game, but the Deleter is thought to be James Pierce for a few evidential reasons. Samus later discovers that these weapons are Metroids that have been genetically modified to remove their weakness to cold, making them vir- tually indestructible. Adam sacrifices himself to detach Sector Zero, the Metroid breeding area, from the main ship and activate its self-destruct sequence. After defeating a Queen Metroid, Samus finds the real Madeline Bergman, who tells her the truth about the android she found earlier. The artificial intelligence, named MB, took on a human shape to build an ideal relationship with the Metroids, similar to the one Samus had with the Metroid hatchling (Super Metroid). After developing emotions, MB revolt- ed, telepathically ordering the cloned Zebesian life forms on the ship to attack their captors. MB appears and attacks Samus and Madeline, but is stopped when Galactic Federation reinforcements show up, led by Antho- ny, the only surviving member of the original squad. Samus, Anthony and Madeline all escape on Samus's gunship. In an optional epilogue, Samus returns to retrieve "something irreplaceable:" Adam's helmet.
Announced at E3 2015, Metroid Prime: Federation Force is a spin off of the Metroid Prime series. The game is a 4 player co-op game focusing on missions. It also features a mode called Metroid Prime: Blast Ball.
In June 2017, Nintendo announced an official remake of Metroid II: Return of Samus for the Nintendo 3DS. It was published on 15 September 2017.