The Mutants are a result of any living creatures that undergo a further mutation whether it may be a exposure to radiation or a failed experimentation. Thanks to these mutations, these creatures possesses a greater unparalleled biology compared to the former, making them extremely dangerous against any humans that have come upon their natural habitat.
In Metal Slug Defense and Metal Slug Attack, all of the mutants belong to the Independent faction.
|Mutated Soldiers: Mutant soldiers as a result of a failed super-soldier experiment created by the Rebel Army. The mutations grant them a decline in intelligence, ability to explode their bodies at will, and cling through walls and ceilings with immense speed.|
|Chowmein-Conga: A small mutated crab born as a result of a Nuclear test on Dr. Moureau's Island. They have a fairly strong carapace and can work together as a group. These mutant crabs can attack with their large claws or spit acid bubbles.|
A red version can be found in Metal Slug Attack where it has a been greatly enhanced but only uses its combustible flame bubbles as a regular attack.
|Ohumein-Conga: A much larger version of their brethren, the Chowmein-Congas. The Ohumein-Congas have greater strength but are mostly solitary hunters. The red version mostly is found in the overground, while the green version thrives from the underground and the brown ones can be found underwater.|
In Metal Slug Attack, a golden variant is also encountered that charges at enemies while rapidly jabbing at them.
|Enormous Moray: An oversized moray eels that lives in the depths beneath the Island. They were tamed by the Rebel Army and given a collar and names. Unlike the previous mutants, these enemies are mostly treated as a timed obstacles rather than a usual enemies.|
In Metal Slug Attack, Elysion summons a cursed moray that spews out jellyfish at enemies.
|Jellyfish: Large jellyfishes that were usually preyed by larger creatures, these Jellyfishes can use bioelectricity with their oral tentacles to generate an electricity around their bodies when threatened.|
An aerial version is also found in Metal Slug Attack and is also dubbed as the "Sky Jellyfish", where it is adapted to live in the sky.
|Flying Killer: The flying killers are a mutant carnivorous fish. They usually work together in packs to attack the player. Sometimes, they are also stored in a small canister.|
In Metal Slug Attack, an evolved group of Flying Killers are encountered, possessing a gray skin and linger longer before exploding. Elysion also summons some cursed Flying Killers to attack her enemies.
|Man Eater: These carnivorous plants are born as a result of a failed experiment performed by the Rebel Army by releasing toxic chemicals on plants. They can swallow the player alive, resulting in an instant death if not avoided. Sometimes upon defeat, they will turn into a larger plant and spew deadly spores. Direct contact with the spores will result in the player turning into a mass of vines and die, otherwise it will drop on the ground and reborn as a new man eater.|
In Metal Slug Attack, a durable purple variant exists, alongside a golden variant developed by the Amadeus Syndicate.
|Huge Locust: A large locust born as a result of a nuclear test or a failed experiment. They can lunge towards the player and feast upon them if not avoided.|
In Metal Slug Attack, a poison variant exists that can nimbly pass through enemy formations to attack deeper.
|Sasquatch: These sasquatches living in cold, remote areas. They emit an icy breath which freezes anything it touches or turns them into a snowman. It will also approach the player and using its large bones as a close range attack.|
In Metal Slug Attack, another group of sasquatches have mutated further in the cold, possessing stronger frost attacks and are capable of calling in their own kind as reinforcements.
|Maggot: Large maggots that are capable of reproducing in an alarming rate. When the player approaches them, they will sacrifice their body and spitting acidic body fluids.|
In Metal Slug Attack, poison and a "tower" of maggots are encountered in the game.
|Big Snail: Malevolent mutant molluscs living near Rebel Army facilities. It spits acids to the player and can also dangle from the ceiling and drop their explosive escargot shells. Sometimes, these snails will hide in their hard shells when attacked.|
In Metal Slug Attack, fire (called "Skull"), poison and golden snails are also encountered in the game.
|Giant Caterpillar: An emormous caterpillar thriving in the underground hive and attacks whoever threatens their territory. It can extend its tongue to spit acidic bubbles or trample the player.|
In Metal Slug Attack, there is also a golden version of this Caterpillar named "Grandee" which is summoned by a girl named Esther. Poisonous and flame caterpillars are also encountered in the game.
|Squid: Squids inhabiting seawaters where the Ptolemaic Army's underground facility is located. They propel themselves towards the player and run over them.|
In Metal Slug Attack, Elysion summons cursed squids called "Titanomakhia" to attack enemies.
|Huge Ivy: These mutated plants inhabiting the Scrap Island's waterfall ruins. It uses its elongated tentacles to trap any living creatures that dares to pass through it. On long range, it can drop down seed bombs.|
|Huge Hermit: The first boss in Metal Slug 3, this hermit crab has evolved to gigantic size and was weaponized by the Rebel Army, allowing it to fire cannon shells and fireballs.
In Metal Slug Attack, miniature, skull, evolved, flying and golden Huge Hermits are also encountered in the game.
|Cyclobster: A large mutant Jellyfish born as a result of a discarded mutant weapon developed by the Rebel Army. This creature can use its large barbed tentacles to attack its enemies. Its tentacles are also armed with paralytic toxins which can stun the enemies.|
|Zoni Doloma: A mutant catfish, this sinister monster can hide underground and uses treasures as a bait to lure its human prey. It can also breathe out debris, junks, and sand.|
|Elder Centipede: A mutant centipede, it is an ancient monster that contains an ancient virus that decimates anything it makes contact with. It relies on its acid spit and mass to defeat enemies.|
|Queen Big Snail: A larger version of the Big Snail, it thrives on the underground. They can use their elongated tentacles to capture prey and leave a poisonous snail trail.|