Normally, the species reproduce via a Queen laying eggs, but if they are exposed to extremely high amounts of Beta-Rays, Metroids are capable of asexual reproduction via division, in a process much like a cell undergoing mitosis. This artificial method of propagation seems to be restricted to the Metroid's jellyfish-like phase, specifically the Infant and Larval stages; whether those in the later stages of their life cycle can be multiplied in the same manner is never stated upon.
The Space Pirates have used beta-radiation on the creatures since the time they stole the first discovered specimens from the Galactic Federation's Space Research Vessel Marina. When the Pirates reached Tourian, their headquarters on planet Zebes, they continued to expose them to beta-rays in order to greatly increase their initially low number of Metroids. This allowed them to perform any number of research and experiments on the species in the hopes of exploiting their unique powers and ultimately achieve ways in using them as bioweapons against galactic civilizations.
This beta-ray method is likely what allowed the Pirates to maintain a steady supply of Metroids throughout the years that covered the entirety of the Metroid Prime series following the downfall of Zebes. Interesting to note is that the highly radioactive mutagen known as Phazon has demonstrated on several occasions the power to multiply strains akin to the Metroid larvae. Interestingly, some mutants created via Phazon exposure acquired the ability to spawn Metroids.
Following the Space Pirate organization's multiple defeats at the hands of bounty hunter Samus Aran and the subsequent destruction of important research bases along with their Metroids, their supply of specimens eventually ran out. To prevent future misuse of the now-dreaded species, the Galactic Federation ordered the extinction of the Metroids on their natural homeworld, SR388; this effectively left the Pirates without a source of specimens until the capture of the last Metroid on the Ceres Space Colony. After successfully stealing it, the Pirates were quick to use the tried-and-true beta-rays on it, only this time instead of equally exposing several Metroids to the radiation simultaneously, the sole Infant served as the entire backbone of the Metroid propagation.
Time would be against the Space Pirates however, and in their desperation to resupply themselves with a satisfactory amount of Metroids before a major retaliation from Samus and/or the Galactic Federation occurred, the marauding race attempted to include genetic cloning alongside the beta-radiation. The clones would turn out to be failures while the Metroids born from beta-rays had no issues, but the problem remained of the last Metroid being the initial sole target of all radiation exposure.
Continued exposure to beta-Rays may have lead to a side effect on the last Metroid in which it unnaturally increased in size. It is never confirmed in official media if the beta-rays was the main factor behind this anomaly. The non-canon Super Metroid comic presented excessive beta-ray exposure as being the sole cause.
It is unknown if the Galactic Federation may have continued to use Beta-Ray exposure over the course of their Metroid Breeding programs on the BOTTLE SHIP and Biologic Space Laboratories research station after the successful cloning of the last Metroid.
- The Metroid: Zebes Invasion Order and Super Metroid Players' Guide backstories imply that the Federation were the first to use Beta-Rays on Metroids when the species was first discovered. This would thus be followed by the Pirates emulating the work achieved by the Federation.
- Due to the seemingly lack of a Queen Metroid on the B.S.L. station (contrary to the BOTTLE SHIP), it is more likely that Beta-rays were used by the Federation within said station.
- It is unknown if the Beta-rays' effect on Metroids was an intended feature implemented by the Chozo when they created the species. If it is the case, it would lean on the theory that the Metroids' life cycle on SR388, and thus the metamorphosis into an egg-laying Queen, was an unforeseen trait that the creatures developed on their own outside of their creators' intentions.