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As with the original game, it only takes 5 Missiles to kill an Alpha Metroid. The more Alpha Metroids Samus kills, the more abilities they gain: in addition to trying to ram Samus, Alphas can also charge at her at high speeds, and will often dart out of the way of missile fire. Some Alpha Metroids have longer horns and small talons, or legs, indicating they are starting to evolve into Gamma Metroids. Two Alpha Metroids are encountered and battled together in the Research Lab sub area, and were likely responsible for the deaths of the Federation research team.
One chamber in the Distribution Center contains five Alpha Metroids at once. Their Logbook entry states that the Metroid larva's transformation into the Alpha stage resulted in the loss of all but one nuclei, leaving its membrane vulnerable to Missiles for all future stages in the Metroid life cycle.
Samus encounters 21 Alpha Metroids during her mission.
It takes 10 normal Missiles to kill a Gamma Metroid. In addition to occasionally pausing to shoot electricity, Gammas further into the game will often dart out of the way of missile fire and can charge at high speeds like the Alphas. If the charge attack connects they can grab Samus and channel their electrical power into her, before dropping her to the ground. Samus will fall back and be unable to move for a few seconds when they do this, although this can be nullified with the difficult to pull off Ukemi technique.
One underwater chamber in the Distribution Center contains a pair of Gamma Metroids, although they are noticeably slowed down by the water. According to the Logbook entry, Gamma Metroids transfer negative electrical charges from their nervous system to their horns, which allows for the electricity to be discharged in an arc of lightning. The exoskeleton has expanded to provide additional protection to compensate for its nuclei membrane, which remains vulnerable. Their legs are long, sharp and spindly at this stage, and the Gamma Metroid uses them to capture prey and drain them of their energy.
Samus encounters 15 Gamma Metroids during her mission.
Zeta Metroids will die after being hit with 20 normal Missiles, although Super Missiles will help to speed up battles with them. In AM2R their behavior is similar to their own in Metroid II and the Omega Metroid from Metroid Fusion, being a land-based bipedal creature instead of hovering in midair. The Zeta Metroid will stomp around its chamber and spit a stream of corrosive acidic saliva at Samus, in addition to slashing at her with its claws, throwing a pair of energy waves, and charging at her at high speeds. It can also nullify missile fire using a swipe, but only not while attacking.
One chamber in the Distribution Center has a Zeta Metroid surrounded by energy cells which it can detonate with its energy waves, which can disable Samus' weaponry if she does not have the Gravity Suit. According to the Zeta's Logbook entry, the Alpha and Gamma Metroid stages are the pupal phase of the species' life cycle, and its evolution into a Zeta Metroid marks the beginning of its adulthood. Its immense weight causes it to lose the ability to levitate.
Samus encounters 4 Zeta Metroids during her mission.
As the apex predator of SR388, the Omega Metroid is the most powerful of all Metroids, before the Queen. In version 1.0 they required 40 Missiles to kill, while version 1.1 reduced the amount to 35 Missiles. In AM2R, like the Zeta Metroid, the Omega Metroid's behavior is combined from Metroid II and Metroid Fusion. It breathes a long stream of fire (an "organic flamethrower") from its mouth, which is actually saliva ignited by the creature's mouth glands.
It also slashes with its claws and jumps around, with the force of its landing knocking Samus off her feet if she is on the ground when it lands. When it lands from a jump, a small, second weak spot will briefly open up on its lower back, which can be targeted for triple damage. The Log entry states that the Omega Metroid's large size is caused when the Zeta Metroid's muscles rapidly expand to massive proportions during its evolution into the next form.
Samus encounters 4 Omega Metroids during her mission.
The Queen Metroid's cell structure is suggested in the Logbook to be very old, perhaps almost as old as the Genetics Laboratory in which she is found, hinting at her being the very first Metroid created by the Chozo. Her genetic coding is distinct from other Metroids and it is suggested that the creature went through a unique life cycle to attain its form. It is the only Metroid in the natural life cycle capable of producing offspring, and the mother of every Metroid on SR388.
The Queen's mobility has been hindered by her time spent in the hive, but this has caused her to develop a long neck and massive head that can strike enemies at a distance, and an impenetrable torso. The Queen is fought in very much the same manner as before, but the battle is expanded. She will launch a number of projectiles from her mouth, which can be destroyed and yield Energy Capsules and ammo (if the Plasma Beam is skipped, the projectiles will not yield any pick-ups, making the battle more difficult). She will then ram at Samus's position with her head several times.
Her weak spot, her head, is vulnerable to Missiles and normal Bombs (Five-Bomb Drops are particularly effective), but only while she is attempting to lunge at Samus. When Super Missiles are used, the Queen's red "eyes" will flash; when Power Bombs are used, her "eyes" will close until after the explosion, but it does no damage. When she has taken enough damage, the Queen will charge a fire ball in her mouth and then launch it at the wall behind Samus, destroying it and extending her chamber which repeats up to four times, reminiscent of the battle against the Metroid Prime.
The Queen will be fought in two corridors and one room where she has more ability to move her head. In the corridors, she will sink or raise her head before launching. In the final room, the Queen will put Samus in her mouth before throwing her away, and can be finished off in several ways. The first way is by shooting 15 Missiles or 3 Super Missiles at her head before she can eat Samus, which will cause her to release Samus from her mouth and shake violently before anticlimactically exploding into a puff of smoke (much like the other Metroids), leaving no trace of herself behind.
The other, more popular way to kill the Queen requires Samus to allow herself to be eaten, entering her stomach with Morph Ball and laying a Power Bomb to instantly finish off the Queen as in Metroid: Other M; her head and backside will be left behind, with green blood dripping from the ceiling. The Power Bomb can also be laid inside her mouth, which will cause her body to go limp, before exploding and leaving no trace of her behind. Finally, normal Bombs can be laid inside the Queen's mouth or stomach until she dies, although again, none of her body will be left behind if she is killed this way. Samus can also unmorph and exit through the Queen's backside if she uses normal Bombs.
It should be noted that the escape route tunnel that was present in the Queen's nest in Metroid II has been removed in AM2R, and Samus's energy is no longer fully restored after the Queen is killed.
The Ancient Guardian is a new boss fought on the way out of the Golden Temple, in a short corridor. It blocks off the corridor on both sides with spike-lined walls and attacks Samus from above. It unleashes several attacks: a quick blue laser burst, a set of six purple fireballs that spread out in the air and then disappear, six green fireballs that impact the ground (only leaving a safe spot under the Guardian) and a yellow fireball that spreads a wave of fire across the ground on both ends. When attacking, the Ancient Guardian is invulnerable to damage, but is otherwise easily destroyed with Missiles.
The Guardian cannot use both features at once due to its archaic design, which constricts it to operating at low power. As the Ancient Guardian takes more damage, the spike-lined walls close in, giving Samus less room to fight. The Ancient Guardian's Logbook entry states it is programmed to detect foreign beings carrying stolen Chozo upgrades; one of the writers of AM2R explains this idea originated from the X Parasites' capabilities of absorbing Chozo items, therefore the creatures' strange body compositions would activate the Guardian. Consequently, Samus's unnatural DNA triggers the boss to attack her as well.
Ancient Guardian shares its battle music with The Tester. The music has been altered with subsequent updates to the game.
According to DoctorM64, the Ancient Guardian was an "improvised" boss from Chozo Statue sprites in Zero Mission.
The Arachnus battle combines elements from the fights against the creature in Metroid II and Metroid Fusion, and has been expanded beyond simply firing at the creature. While on the ground, it will launch fireballs at Samus or its slashing attacks from Fusion; unlike Fusion, it fires red fireballs with wide gaps in between their flaming spots or green fireballs that bounce around Arachnus' room, and its slashing attacks have no wind-up and can be fired diagonally upward.
It can also curl into its ball form in the air and launch itself at Samus, in a similar manner to Sonic the Hedgehog's Homing Attack (and a scrapped Boost Ball function in Metroid Prime 2: Echoes). After it sustains enough damage, it will roar, become invulnerable, and begin to ram into Samus in its ball form. Samus must lay Bombs in a fashion that the Arachnus will be launched towards a set of twelve mounted electrified spikes on the walls. After it hits one set, the bottom-most set disappears and the Arachnus takes damage.
If Samus takes too long to launch Arachnus, it will briefly uncurl to launch fireballs that move horizontally at standing face height and bounce along the walls, which can be avoided by staying in Morph Ball. After it is damaged by the last set of spikes, Arachnus will die and leave the Spring Ball as a reward. According to the logbook, Arachnus' power and agility are stated to be a result of the item it carried.
When battling Arachnus, a remix of its battle theme from Fusion plays. On Fusion Mode playthroughs of the game after subsequent updates, Arachnus becomes a Core-X after its initial defeat, which must be destroyed by Samus.
The Torizo, a more advanced version of the animated Chozo Statues from Super Metroid, is fought in the beginning of the Industrial Complex, after Samus acquires the Space Jump from its hands. A Logbook entry states that this Torizo is partially organic, with a concentration of organic matter on its chest constituting a weak point. This is further implied to be the case for other Torizos, such as the ones fought in Super Metroid.
This Torizo is initially fought much like its Zebesian brethren, with its upper body being the main target and its attacks consisting of energy waves and fireball projectile volleys. However, its energy waves curve in a similar manner to the Wave Beam instead of moving straight. The Torizo walks much faster the more damage it takes, up to the point where it matches Samus's running speed, although Samus can duck under its legs using the Morph Ball. After taking enough damage, the Torizo will appear to be destroyed. After a moment of silence, though, the music will return, faster than before, as the Torizo deploys mechanical wings and a jetpack to take flight.
The ceiling rises with it, revealing platforms in the air, and spikes will begin to emerge from the ground. Samus must use the Space Jump to destroy the Torizo in its second form. While only its upper body was vulnerable to attacks in the first phase, its entire body can be attacked in the second phase. In this second phase, it will no longer fire energy waves, but instead spit a continuous stream of fireballs, fire egg-like objects from its stomach that hatch into small birds which briefly chase Samus before disappearing, and attempting to ram into Samus at high speed four times in succession. Its projectiles can be destroyed for Energy Capsules and Missile Ammo. The Torizo's sprites were designed in 2012.
According to DoctorM64, the Torizo originally had wings, but they were difficult to animate, so he ended up giving it a jetpack. He also experimented with a skeletal look for the mechanism. 
The Torizo's battle music is a remix of the Chykka theme from Echoes, even picking up in tempo after the mechanism's wings activate. This is similar to the Chykka's theme increasing in speed after the Larva is defeated and the Adult emerges. On Fusion Mode playthroughs, Torizo transforms into a Core-X after its defeat.
The Tester is a spherical mechanism present in a very tall shaft in The Tower. It was created for AM2R. The Logbook states that it performs 360° live-fire tests of prototype weapons. It is a sphere that floats up and down in its chamber, guarded by four side plates, which are resistant to beam weaponry and are used in a drilling-like attack. It also spins in its position while firing streams of missiles as well as the Ice, Wave, Spazer, and Plasma Beams from its four turrets, which can be destroyed for pickups.
To defeat the Tester, the side plates must be destroyed with missiles, along with its interior shield with beam weaponry, and finally the core of the machine itself. However, the interior shield has an auto-repair system, and will regenerate over time on Hard Mode. Partly helping Samus stay close to the machine in the air are numerous Proboscum mechanisms on the walls. The Logbook reveals that this was applied after earlier models' cannons were unable to stand up to exceedingly violent tests; the logbook writer explains he envisioned the Chozo trying out the effectiveness of various weapons against captured X Parasite specimens.
Much like Samus's Power Suit, the Tester's design allows for the assimilation and removal of equipment. The Tester shares its battle music with the Ancient Guardian. DoctorM64 later said that the Tester was an "excuse for Samus to use all her weapons", meaning all of the Beams she had acquired by that point.
On Randomizer playthroughs of AM2R, the Tester can be killed instantly with a Power Bomb.
The Tank Prototype is a new boss battled during the escape from the Power Plant. The prototype attacks with missiles and beam projectiles; the former can be destroyed for pickups. Sensors on its head allow it to aim accurately at Samus, although its armor has weakened over time. It will also slowly move toward Samus, destroying the generators on the ground along the way. Its head, arms and base can be destroyed, which will stop it from accurately targeting, firing beam projectiles, and moving respectively. The prototype's chest is its weak spot, and is guarded by a destructible chest plate.
The Logbook states that this mechanism was planned to be mass-produced and remote-controlled by the Chozo, however a basic A.I. is now active due to a lack of commands. Although the AM2R logbook writer intentionally left the machine's purpose highly ambiguous, he stated that the Chozo designed it to be remote-controlled in order to remove the need for live pilots in the battlefield, thus preventing both infection and their Tanks being turned against them when they would have been launched against X Parasites; this mass-production never came to fruition due to the creation of the highly efficient Metroids.
The Genesis enemy encountered in Metroid Fusion is fought as a miniboss inside the G.F.S. Thoth, having escaped from one of the specimen tanks within the ship. Genesis is blind and relies on its hunting senses. Unlike its official counterparts from Fusion, it is agile and stronger, and attacks Samus in the open. Its entire body is weak to damage, forcing it to conceal itself in the shadows in an attempt to avoid harm. It climbs the ceiling and frequently drops down to spit a barrage of corrosive acidic blood via auto-hemorrhaging as its main attack, or slash Samus if she gets too close.
The Logbook entry for this creature states that it naturally hunts in groups and has little need to evolve. Its name is revealed to be derived from its DNA, which analyses indicated that it belongs to the oldest living lineage on SR388. According to DoctorM64, programming of Genesis was finished in the span of a few hours, only a week before the game's release.
The creature's battle theme is a remix of the Thoth theme, an original composition for the game. When defeated on Fusion Mode, Genesis turns into a Core-X. Its movements and acid breath are very similar to the titular creature from the Alien films.
Serris, a boss from Metroid Fusion, is fought in an underwater room in the Distribution Center. Serris is the fastest animal on SR388. The skin on its underside, a respiratory organ, can be frozen over with the Ice Beam and attacked with Missiles or Super Missiles to nullify its hardened skin and render it vulnerable to attack. It will swim through the water and destroy platforms made of Missile Blocks as it navigates.
As Serris takes more damage, it begins to swim faster, but cannot use the Speed Booster like in Fusion. After its death, it segments will detach and float in the water for a few seconds before exploding. The Logbook reveals that a Serris will move to another location by digging passages to channel water from its previous home to its new one; this is speculated to be the cause of the Distribution Center's flooding.
DoctorM64 later said that he felt Serris was too easy, and would have increased the difficulty of its fight if he was allowed to update the game. He also considered adding a cutscene where a Serris specimen is eaten by an Omega Metroid, showing the latter to be at the apex of SR388's food chain. Later updates improved the battle by restoring Serris' speed-boosting abilities (which it uses for longer than it does in Fusion) and allowing Samus to shoot the tunnels it emerges from, so they emit electricity that damages Serris.