Of all the mainline Nintendo series, Metroid might be the one with the most even timeline. All of the games fit together, and all without the need for branching timelines like with The Legend of Zelda. Even the Prime series, which is sometimes seen as separate from the main Metroid series, fits right into a specified slot in the Metroid timeline.
Every Metroid Game in Chronological Order
The flagship entry of the Metroid timeline involves Samus' first trip to planet Zebes. She fights several villains here that would reappear later on in the series, including Kraid, Ridley, and Mother Brain. The Zero Mission, which is shown in a remake of Metroid for the Game Boy Advance, reveals that Samus conducted a mission in the Zero Suit after the defeat of Mother Brain. Be warned: massive spoilers for the entire series are found in this timeline.
According to the timeline, Samus gets the distress signal for the Frigate Orpheon right after the events of the first Metroid game. When she investigates, the frigate explodes, leaving her stranded on planet Tallon IV. Here, Samus uncovers the mysteries behind Phazon, and how the Space Pirates are using it to create bioweapons. At the end of the game, she defeats Metroid Prime in battle, but some of Samus' DNA is infused with Phazon.
Metroid Prime 2: Echoes
This game follows Samus as she answers the call of the Luminoth, a species on planet Aether that is being oppressed by the Ing, a warmongering alien race. The planet of Aether is split into Light and Dark modes after suffering impact from a Meteor. Samus eradicates the Ing from the planet, later facing Dark Samus, which is the result of her DNA mixing with Phazon from the first Metroid Prime game.
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Metroid Prime 3: Corruption
In this game, Samus becomes corrupted with Phazon herself, giving her access to the PED, an enhanced suit that can use a beam similar to the Hyper Beam from Metroid Prime. After traveling to several new planets, she arrives at Phaaze, the home planet of Phazon. There, she has a final duel against Dark Samus. In a secret ending, an enemy named Sylux is shown pursuing Samus as she leaves the planet Elysia.
Metroid Prime: Federation Force
After the events of Metroid Prime 3: Corruption, the Space Pirates appear to still pose some threat. In response, the Galactic Federation sends some soldiers in Mechs to finish off the Space Pirates. Samus is seen helping out at times during the mission. Eventually, the soldiers find Doomseye, a huge Space Pirate ship. The soldiers blow up the spaceship, but at the end of the game, Sylux is seen again, this time hatching a Metroid egg.
Return of Samus/Samus Returns
At this point, the Metroid are deemed too dangerous to exist by the Galactic Federation. Therefore, Samus is charged with traveling to SR388, the home planet of the Metroids, to eradicate them completely. She eventually finds the Metroid Queen and defeats her, but on the way, she finds a baby Metroid who appears to take a liking to Samus. This hatchling would be referred to as "The Baby" from this point onward.
Samus takes The Baby back to the Galactic Federation for further study, but Ridley shows up, kills several scientists, and takes The Baby for himself. Samus chases after Ridley, who has returned to a rebuilt planet Zebes. This puts her in another showdown with Mother Brain. At first, Mother Brain almost kills Samus, but The Baby sacrifices itself to give Samus another shot. Upon its death, The Baby grants Samus access to the Hyper Beam, which is powerful enough to beat the new Mother Brain. Samus then escapes Zebes as it blows up again.
Metroid: Other M
After Super Metroid, Samus answers a distress signal from The Bottle Ship. There, she finds Galactic Federation soldiers along with Adam Malkovich, a former commander and somewhat father figure. Samus learns that The Bottle Ship has be constructed to be some version of Zebes, filled with Space Pirates and even Ridley. They have also created Metroids which can't be frozen, which causes Adam to blow up a sector of the Bottle Ship, sacrificing himself in the process. Afterwards, Samus defeats an AI called Madeline Bergman, who serves as a new Mother Brain. Madeline Bergman's demise causes all other enemies on the Bottle Ship to stop functioning, although some enemies still remain as part of a post-game mission.
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Galactic Federation Scientists discover that Samus was infected with an X parasite during her travels in planet SR388. In response, the scientists infuse Samus' Power Suit with Metroid DNA, giving her immunity. The parasite then becomes a mirror image of Samus, known as the SA-X parasite. This parasite attacks the BSL (Biological Space Laboratories), which Samus then investigates, defeating the SA-X in the process. On the BSL, Samus can communicate with Adam (likely Malkovich from Other M) via computers. This mechanic would reappear in Metroid Dread.
After the events of Metroid Fusion, Samus gets a different distress signal from planet ZDR, which has been taken over by Raven Beak. The planet is guarded by seven EMMI units; powerful robots that are immune to most of Samus' weaponry. Upon exploring more of ZDR, Samus discovers that the X parasite is present, and Raven Beak releases them into the wild from Elun, a secret area on the planet. Raven Beak (who is actually Samus' father) actually tries to turn Samus into a Metroid, which happens when she gets the Metroid Suit. Samus uses the suit, however, to defeat Raven Beak and escape the planet.
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Metroid Timeline, Explained