The Metroid capsule was a Galactic Federation capsule containing a captured Metroid from SR388. Loaded aboard the Space Research Vessel Marina, it was to be brought back to Galactic Federation Headquarters for study when the ship was attacked by Space Pirates. They stole the Metroid and took it to Zebes, seeking to multiply it and use it as a bioweapon. This set in motion Samus Aran's Zero Mission. According to the Metroid II: Return of Samus manual, the capsule placed the Metroid into stasis.
|“||"The command room, now destroyed to hell. The Pirate Boss was alone, smoking a cigarette. ...I must retrieve the capsule!"||„|
—Samus Aran, page 87
In Zebes Invasion Order, several Metroids are obtained in ecology capsules and the Marina is not attacked. One capsule containing a developed, seemingly dead Metroid is studied by a team in the Special Investigations Group. It is discovered in a trial run on the Metroid that it can be resurrected within 24 hours with exposure to Beta-Ray radiation. This Metroid annihilated the research team, before it was killed by the 3rd Division of the Federation Space Army.
The Pirates later steal a capsule and bring it to Zebes, and the Federation assumes it is being kept in their stronghold. After destroying Mother Brain, Samus attempts to recover the capsule from the Pirate Boss, the Space Pirate responsible for stealing it. However, the Metroid inside had mutated into a massive beast that Samus dubs Metroid=Mutant, or M=M, and it engages her at various points.
The baby is kept in a similar capsule in the introduction of Super Metroid during the Space Science Academy's study of it. When Ridley captures the infant Metroid, the creature remains in its capsule. During the first battle with Ridley, the capsule can be temporarily dislodged if he suffers enough damage, but he will quickly pick it back up and flee. Samus later finds the capsule broken, and the hatchling missing, after defeating Ridley in Lower Norfair. The hatchling is re-encountered in Tourian, having grown exponentially similar to M=M.