Born from the stolen Metroid capsule, M=M mutated drastically, developing large crustacean-like limbs; long tentacles; several massive eyeballs inside of its main body; and a dramatic increase in overall size compared to other Metroid larvae. Its exterior is resistant to the Ice Beam (although its internal organs are still vulnerable), although it can be temporarily defeated with missiles. It seems to possess a degree of sentience, since it exhibits signs of malice and regards Samus Aran as its nemesis.
Samus first encounters the M=M aboard her gunship after she retrieves the Metroid capsule from Zebes. After this, she can run into M=M at different points, with the choice to fight or flee; sometimes, M=M itself will flee.
With the M=M loose aboard her gunship, it can cause damage to the ship's energy tanks, engine, and oxygen tanks. Samus's options include sending out a distress signal from her cockpit, or evacuating in a smaller Escape Pod while the heavily-damaged gunship explodes. In the former scenario, the M=M is briefly scared off when the distress signal is received by an enormous Pirate Ship. In the latter scenario, the M=M sneaks aboard her Escape Pod, forcing Samus to open the airlock (she can either expel the M=M out of the pod, or evacuate the pod herself). Samus can only successfully kill the M=M by trapping it inside her gunship as it explodes, but this results in a Bad Ending where the Metroid capsule is also lost.
Afterward, the M=M boards the Pirate Ship and wreaks havoc, killing Space Pirates in its path. Depending on Samus's choices, she may team up with the Space Pirates to an effort to defeat the M=M as it attacks the control room, with the Pirate Boss returning her confiscated Ice Beam and missiles.
In the Good Ending, the M=M interrupts the sword duel between Samus and the Pirate Boss in the control room. With the Pirate Boss distracted, Samus takes the opportunity to retrieve the Metroid capsule and flee the Pirate Ship. Although she destroys the Pirate Ship with a large missile, the epilogue implies that the M=M survives and is seeking its nemesis.
In the Bad Ending, the M=M encounters Samus in the ship's docking bay and acts as the game book's final boss. If Samus fights the M=M, it may latch onto her, giving her the opportunity to fire her Ice Beam and missile inside the creature. If she runs, she may retrieve her equipment and fire a Gravity Bazooka at the M=M, stunning it long enough for her to escape. Either way, she escapes in a small spacecraft and destroys the Pirate Ship, but she fails to retrieve the Metroid capsule, and the surviving M=M has latched onto her escape ship.
- M=M can be considered a non-canonical predecessor to the Big Metroid seen in Super Metroid, since each specimen is a supersized mutant Metroid that was formerly contained in capsule stolen by Space Pirates; both are resistant to the Ice Beam; and both also have a strong connection to Samus, to the extent of interfering with a climactic battle between Samus and the leader of the Space Pirates. However, it is unknown if Zebes Invasion Order had any influence on the development of Super Metroid.
- Similarly, it could also be a non-canon predecessor to Dark Samus, as both were mutated Metroids (or in the case of the latter, a reincarnated version of a heavily mutated Metroid) that have an obsession with viewing Samus as their arch-nemesis. The ending narration also implies that the M=M regenerated from being blown up by a missile from Samus alongside the pirate ship, similar to how Metroid Prime ultimately survived the Tallon IV Impact Crater collapsing on it, as well as Dark Samus's similar survival of the collapse of Dark Aether, both of which Samus had been responsible for causing.