- Metroid and Metroid: Zero Mission (1986/2004)
- Samus travels through the caverns of the planet Zebes to stop the Space Pirates from exploiting the Metroid species for galactic domination. She confronts the cybernetic lifeform Mother Brain, as well as its guardians, Kraid and Ridley. In Metroid: Zero Mission, it is revealed that afterwards Samus was ambushed by Space Pirates after defeating Mother Brain and escaped from Zebes, and her ship crash-lands back on the surface. Stripped of her Power Suit and her gunship destroyed, she is forced to infiltrate the Space Pirate Mothership in order to find a way off the planet with only an emergency pistol for protection. After receiving a fully-powered suit from deep within theChozo ruins, she steals an escape pod from the Space Pirate Mothership, as well as triggering its self-destruct sequence after eliminating Mecha-Ridley.
- Metroid Prime and Metroid Prime Pinball (2002/2005)
- Samus receives a distress signal and travels to Tallon IV to stop the Space Pirates from exploiting a powerful radioactive substance known as Phazon. She discovers that the ancient people who raised her and bestowed her with the Power Suit, the Chozo, once settled on Tallon IV, and their disappearance, as well as the emergence of Phazon, is due to a meteor crashing on the planet at an unknown date. The Chozo sealed away the source of the Phazon, and left the planet. Their prophecies foretold Samus' arrival, and they left her numerous weapons to help her defeat the source of the Phazon. After gathering all the abilities, having her suit corrupted by Phazon and collecting the 12 artifact keys, she unseals the Impact Crater and confronts Metroid Prime, a mutated Metroid and the source of the Phazon. After killing it, Metroid Prime absorbs Samus's Phazon Suit, and dies. However, collecting 100% of the items reveals that Metroid Prime's death has yielded the birth of a new enemy: Dark Samus.
- Metroid Prime Hunters (2006)
- When the Galactic Federation receives an unusual telepathic message, Samus is sent to the remote Alimbic Cluster in the Tetra Galaxy to uncover the rumored "Ultimate Power". Six rival bounty hunters that also heard the message attempt to secure the power before anyone else, including Samus. It transpires that the promise of Ultimate Power was actually a lie sent by the creature Gorea, sealed away by the Alimbics in a void between dimensions. After defeating Gorea, Samus and the other hunters are believed to have escaped the Oubliette. What occurred to the Omega Cannon after Gorea's defeat is unknown.
- Metroid Prime 2: Echoes (2004)
- Samus is sent to investigate the planet Aether after communication with a squad of Galactic Federation troopers was lost. Samus finds them all dead, killed by several creatures, mainly consisting of an evil race called the Ing. Upon meeting one of the several remaining members of the Luminoth race, U-Mos, Samus learns Aether has been split into two dimensions by a meteor similar to the one that crashed on Tallon IV. Samus helps save Aether from the Ing, but encounters Dark Samus along the way.
- Metroid Prime 3: Corruption (2007)
- The third and final chapter of the Metroid Prime trilogy. Samus and three other Bounty Hunters are called upon by the Galactic Federation to repair an Aurora Unit and investigate Pirate operations. The Pirates attack the nearby planet Norion during the briefing. Samus and the hunters restore the defense cannon but a Leviathan launched by Dark Samus and the Pirates threatens to corrupt the planet. On their way to the cannon, Samus and the hunters are corrupted by Dark Samus. Samus manages to destroy the Leviathan just in time. A month passes and Samus is given a new suit and a new mission : To destroy the Leviathans and discover what happened to the other hunters that the Federation lost contact with on three worlds; Bryyo, Elysia and the Pirate Homeworld. But time grows short as Samus herself struggles with her own corruption. She eventually travels to Phaaze, source of all Phazon. She destroys it and Dark Samus, thus destroying all Phazon in the universe.
- Metroid II: Return of Samus (1991)
- Following the events of the previous chapters, the Galactic Federation deems the Metroid species too dangerous to exist, and, after their own failed attempts, employ Samus to travel to the Metroid homeworld, SR388, and exterminate the entire species. After killing every Metroid, Samus finds an unhatched egg sac. As she prepares to destroy it, a Metroid larva pops out and believes Samus is its mother. It follows her back to her ship, and Samus hands it over to the Galactic Federation for research.
- Super Metroid (1994)
- Samus receives a distress signal from the research lab where she took the Metroid hatchling at the end of the previous game. She returns just in time to see Ridley stealing the hatchling. She then follows Ridley to the rebuilt base on Zebes to stop the Space Pirates in their new plan to clone the Metroids and use them as a weapon. She kills the reborn versions of Ridley, Kraid, and Mother Brain, blowing up Zebes and killing the last remaining Metroids.
- Metroid: Other M (2010)
- (This story is not completely understood yet, though it is set to explain the past of Samus Aran and Adam Malkovich, as well as cover events bridging Super Metroid andMetroid Fusion.)
- Metroid Fusion (2002)
- While acting as a bodyguard for researchers on the planet SR388, Samus is infected by a creature known as the X Parasite, the original prey of the Metroids. Doctors surgically remove Samus's Power Suit and cure the X infection with a vaccine created from Metroid DNA, allowing her to survive the parasite. She is then sent to investigate a disturbance at the Biologic Space Laboratories research station, where researchers attempted to contain the infected Power Suit. It turns out that the infected suit became an X mimicking Samus, the SA-X. This released other X parasites inside the other specimins, and began to infect the entire station. Samus attempts to stop them, but eventually decides, with the help of her computer Adam, to crash the station into SR388, killing both the X on the station, and on the planet.
Metroid Prime Pinball is not a separate canon game in the Metroid storyline but actually retells the story of the original Metroid Prime in pinball format. It includes several of the same bosses and areas, such as Phendrana Drifts, Thardus, and Metroid Prime. Despite playing as a pinball game, there are a number of powerups that can be collected in the multi-game mode, including missiles and power bombs.
Copied from http://metroid.wikia.com/wiki/Metroid_timeline.
