As an environmental feature
If Samus stands in a flame, in most games her energy will slowly deplete, with her not making any sound; this may be because the Power Suit is preventing the fire from directly harming her, unlike other attacks. Examples of open flame in Metroid Prime 2: Echoes include that on Samus' Gunship (which disappear with sufficient auto-repairs) and in the ruined Main Reactor after the first battle with Dark Samus, where the pillars surrounding will likely have been destroyed.
One room in Ridley's Lair features Puromi, round objects or creatures that greatly damage Samus unless she passes through them with the Screw Attack. These float in a circular motion and may be related to Polyps.
Fuel Gel, while not a true form of fire, ignites when shot at. Proximity to explosions of Fuel Gel cause great damage.
In the superheated areas of Sector 3, fire periodically explodes from pools of lava. If they hit Samus while she is climbing over the lava via Ladder, she will be hurt and fall into the lava, where she will be damaged even further.
The Metroid Prime and Metroid Prime 3: Corruption Plasma Beam, in contrast to its green piercing effect in other games, takes on a fire theme, with shots being able to ignite and burn enemies and objects. In Prime, the Plasma Beam has the Flamethrower, a Sustained Fire Charge Combo that depletes her Missile supply while allowing her to unleash a stream of flame, though it is only effective on a swarm of small enemies.
The Trooper Pirates and Metroid Prime also possess Plasma Beam attacks similar to Samus, with the Pirates' being a reversed engineered version of her Beam (in the NTSC version of Prime, Metroid Prime was stated to have been captured from the Impact Crater to the Phazon Mines only for it to escape and assimilate Pirate technology, but as the PAL and Wii versions have effectively retconned this with altered Chozo Lore and Space Pirate Data it is no longer known how Prime has a Plasma Beam). Prime can also spawn Plasma Beam Particle Waves which will ignite Samus unless she destroys them. In Corruption, Samus has to kill Ghor for his Plasma Beam when he destroys SkyTown's network circuitry.
Mellas, Multiviolas, Magdollites and Sovas are all creatures that are made of flame and lava. In Metroid: Other M, Sovas can be "cooled" (that is, their fire dispersed) with a shot of the Ice Beam, which usually kills them.
Dragons and their bipedal counterparts, Alcoons, as well as Funes, Namihe and Dragotix spit fire at Samus on Zebes. The Fune, Namihe and Dragotix attack with blue flame, which interestingly is hotter than red, next to white (which is seen with the Light Beam). Additionally, Magmoors breathe flame, and ironically are vulnerable to the Plasma Beam. The Goyagma often slams its hands down on top of the Crater Interior where it is fought, triggering a fiery geyser.
The Bounty Hunter Spire, the Alimbic Psycho Bit v3.0, the Red Barbed War Wasps, Magma Voldrums, Guardians and Gorea utilize the Magmaul, a fiery lobbing weapon that Samus can obtain for herself and use. It is particularly effective on Judicator users, namely, Noxus, due to the contrast of fire and ice. The Fire Spawn is the Magmaul's guardian, and must be killed before Samus can obtain the weapon. The Slench is also capable of fire attacks.
When one of the orbs in Mogenar's body is destroyed, its slot will be lit aflame.
Ridley demonstrates the ability to breathe fire as an attack in all of his appearances. The 2-D games have him unleashing spinning fireballs that Samus can either freeze or destroy (sometimes they net Energy Capsules or Missile Ammo), but as Meta Ridley, Omega Ridley, Proteus Ridley and his clone in Metroid: Other M Ridley unleashes far more devastating attacks (due to the higher capability of the 3-D console games) such as fire beams or in the case of Other M and Samus Returns a large fireball shockwave, which Samus must jump over.
Phantoon's signature attack is the consistent release of "tears", blue eyeball flames in both Super Metroid and Other M. Also in Other M, the Queen Metroid breathes a stream of fire, turning her head across the room. Though Samus successfully SenseMoves over the attack in a cutscene, the attack cannot be dodged as such in gameplay.
The B.O.X. Security Robot, in its first encounter, will launch metal balls that explode into flame currents that shrink and increase while moving across the ground, posing a threat to Samus.
In Metroid: Samus Returns, certain "Evolved" Alpha and Gamma Metroid variants can produce fire instead of electricity. Zeta, Omega, and Queen Metroid can also breath fire. Wallfires are Chozo designed security systems that emit either streams or balls of fire. Proteus Ridley can also breath fire like his previous incarnations.
In the Super Smash Bros. series, Samus' forward air attack (a series of explosions from her Arm Cannon) is called the "Flame Thrower" in strategy guides. In Super Smash Bros. for Nintendo 3DS and Wii U, her forward smash has a fire effect.
|Hazardous||Acid (Beta/Fake) • Acid Rain • Afloraltite • Dark Water • Fire • Fuel Gel • Lava (Fake/Scalding-hot) • Phazon • Purple liquid|
|Gases||Dark vapor • Industrial-grade pesticide • Meta-viprium gas • Nohadin gas • Noxious gasses • Poison gas • Talvania Gas|
|Destructible||Barnacle-like material • Bendezium • Brinstone • Cordite • Denzium • Frigidite • Glass • Grobnite • Ice • Maldium • Meltable Metal • Metroid webs • Radion • Sandstone • Talloric Alloy • Vegetation • Zebetite |
Kelbium and Zafrite
|Phazon||Red • Crystal • Black Crystal • Mass • Ore • Elite Nutrient Mix • Strain Vertigo • Phazite (Red) • Concentrated|
|Crystals||Ammolite/Witherite Shards • Black Phazon • Crystallized Fuel Gel • Crystals • Dark Sentinel • Lift • Liftvine • Light • Minerals • Phazon • Red magma • Sentinel|
|Ore||Urthic • Phazon|
|Miscellaneous||Invisible platform • Jovian steel • Liquid Resource • Liquid solution • Sand |
Vaccine "Metroid" • Waste • Water • Yellow goo • Yellow liquid