I think the film Alien had a huge influence on the production of the first Metroid game. All of the team members were affected by HR Giger's design work, and I think they were aware that such designs would be a good match for the Metroid world we had already put in place.
Both Metroid and Alien feature a female lead protagonist, Ellen Ripley in Alien, Samus Aran in Metroid.
The director of Alien is named Ridley Scott. A miniboss in Metroid (who became an antagonist in later games) is named Ridley.
Nostromo's ship computer is called "Mother". Antagonist of Metroid is Mother Brain.
Alien features eponymous creatures also called Xenomorphs, whose first stage of life latches on to the face. Metroid features eponymous creatures that latch onto the head (faces in the Metroid Prime series).
The end of the film shows Ripley barely escaping from the exploding Nostromo. The end of the game shows Samus barely escaping from the exploding Tourian facility. Both characters are the sole survivors of the explosion (apart from Ripley’s cat, Jones).
Ripley ends up scantily clad near the end of the film. Samus ends up scantily clad near the end of the game (if certain requirements are met).
Ridley slightly resembles a Xenomorph.
The Aliens can shoot out a smaller mouth which is round and has many teeth. The design of the Metroids is similar to this.
The design of the Chozo Statues is possibly based on the fossilized Engineer found in Alien.
Parker constantly suggests to the rest of Nostromo's crew that they should "freeze" Kane, who has a Facehugger attached to him. This may have inspired the Metroids' weakness.
Samus's gender was either hidden or falsified in the manual, depending on the region the game was released. In the Alien script, Ripley's gender was not specified.
In Aliens, Ripley travels to the source of the Alien species, LV-426. In Metroid II, Samus travels to the source of the Metroid species, SR388.
Both center around the female lead attempting to exterminate the eponymous species of their franchise.
Aliens go through a life cycle beginning with hatching out of an egg and then metamorphosing. Metroids also go through the process of metamorphosis.
Both the Metroids and Aliens molt and outgrow their shells as they mature.
The Zeta Metroids are known to spit a type of damaging fluid. The Xenomorph in Alien3 has been shown to spit acid as a form of attack.
The aforementioned Metroid also bears some resemblances to the Xenomorph species in terms of physical features, but the Omega Metroid in particular bears a close resemblance.
Aliens features a final battle with the Queen Alien, the very Alien producing the entire species. Metroid II features the Queen Metroid, similarly.
It is implied when entering Phase 9 that the Queen Metroid had not only promptly birthed 9 extra Metroid Larvae of her own will, but also dispatched them throughout the area as a final line of defense. This is similar to how the Queen Alien was implied to command her eggs to hatch in the climax to Aliens. Similarly, the Queen was also implied by her attacking Samus and the discovery of the Metroid egg behind her to be extremely protective of her offspring, similar to the Alien Queen in the same movie.
Ripley saves and bonds with a surviving colonist, a young girl nicknamed Newt. Samus saves and bonds with a newly-hatched Metroid, nicknamed "Baby".
Once again, Ripley ends up scantily clad at the end of the film and Samus ends up scantily clad at the end of the game if certain requirements are met.
This game heavily implies that the Chozo were responsible for the Metroids creation, which was similar to the pre-Alien: Covenant theory that the Space-Jockies were responsible for creation of the titular Xenomorphs.
In Alien3, Newt is killed. At the end of Super Metroid, the baby sacrifices itself. Ripley also sacrifices herself at the end of the film.
In the Super Metroid comic, Samus’ appearance was a mix of Ripley’s as well as Princess Leia from Star Wars.
In the comic, Mother Brain attempts to convince the Baby that she, not Samus, is its mother to no avail, similar to how the Alien Queen in Alien Resurrection attempted to have the Newborn bond with it instead of with Ripley, but failed.
Kihunters have the ability to spit acid at Samus. The Alien in Alien3 spat acid in one instance at the face of the prison janitor.
The way Kraid can fire spiky projectiles out of his stomach is a possible reference to how the aliens in the Alien series burst out of people's stomach.
One of Ridley's signature attacks, lunging his barbed tail at Samus, is shared by every stage of the Xenomorphs, who similarly use their tails as weapons.
In the final countdown, Samus takes a detour to save the Dachora and Etecoons; in Alien, Ripley takes a detour to save Jones.
In Alien Resurrection, Ripley is cloned and an Alien Queen embryo is surgically removed from her body. It leaves behind DNA that turns Ripley into an Alien/Human hybrid. Similarly, parts of Samus' Power Suit are surgically removed when she is at risk of death, and she is given a Metroid vaccine created from DNA cells of the Baby, turning her into a Metroid/Human hybrid.
The Genesis creatures pay homage to the locomotion of the Alien creatures in the films.
Serris has a clear plate on top of its head, making its brain visible. In the Alien franchise, some Xenomorphs are depicted with the plate on top of their head being transparent, allowing one to see their brain.
The appearance and lunging attack of the Fune/Nahime may be a reference to the inner jaw of the Alien.
Weyland-Yutani clones the Aliens from Ripley's embryo for use as bio-weapons. The Galactic Federation uses the Baby's cells to also create the Restricted Lab that Samus later discovers and destroys.
Interestingly enough, the Federation already seems to possess a bio-organic weapon for military purposes, the Nightmare.
The Alien creatures do not attack Ripley due to them thinking that she is one of them. The Metroids do not attack Samus for the same reason, with the exception of the Omega Metroid.
The scene where Samus discovers the Restricted Lab may have been inspired by the scene in Resurrection where Ripley discovers the lab containing her seven predecessor clones, all of which are heavily deformed. Both laboratories are ultimately destroyed by the female protagonist.
The Federation also wants to use the X Parasites (including the SA-X) for military purposes, similar to the intentions of the Weyland-Yutani company throughout the Alien films.
The escape sequence for Fusion is strikingly similar to that of Aliens. In both sequences, Ripley/Samus are left stranded with no means of escape, and the Queen Alien/Omega Metroid attacking them. At the last minute, their ship flies in and rescues them, and they escape the station.
The Auriga spaceship that the entire film took place on is set by the android Call to collide with Earth. The Biologic Space Laboratories research station is set by Samus to collide with SR388. Both are done to prevent the antagonistic organizations from getting their hands on the Aliens/X.
Samus distrusted her ship's computer, but later came to accept and trust it after it was revealed to be Adam Malkovich. Similarly, Ripley distrusts Bishop 341-B, an android, due to experiences with another android in Alien, but he later redeems himself and earns Ripley's trust.
The X Parasites spread in a similar manner to the Xenomorphs in the Alien series. In this instance, Samus is infected and her infected suit parts are sent to the BSL, while in Alien Kane is brought on board the Nostromo with the Chestburster inside him. Both events set the respective plots in motion. In Aliens, Newt's father is infected and brought back to the colony, therefore starting the whole infestation and deaths of everyone except for the protagonists.
In addition, both lifeforms parasite their hosts from within their bodies and eventually kill them upon reaching a mature stage, with differences, since it's more graphic in Alien than it is in Metroid.
In the beginning of the game, the survivors are all but rumored to be dead. However, Etecoons and Dachoras somehow managed to survive the X infestation for unknown reasons. This is synonymous with Newt, who was the only survivor of the colony during the infestation in Aliens. Additionally, both eventually escape the colony in the end.
Each shoulder of the SA-X's final form resembles the head of a Xenomorph.
The body of the Baby Sheegoth creature somewhat resembles the head of the Alien.
A room called Air Lock is a possible reference to the air locks that are often used at the end of Alien films to destroy an Alien.
Before detaching from its egg sac, the body of the Queen Xenomorph seems to be an obvious inspiration for the design of the titular Metroid Prime.
The opening sequence of Metroid Prime bears a big resemblance to the first movie’s opening. (Shot of the space, Planet Tallon VI in the background)
Frigate Orpheon is heavily influenced by the design of hallways in Aliens. Hallways are hexagonal shaped, just like in the second movie. Some creatures walk around the ventilation ducts just like Xenomorphs.
Pyonchi, Samus' Rabbilis pet, serves the same role as Ripley's cat Jones, being the pet of the main character. Both Pyonchi and Jones survive life-changing events along with their owners, and are left in the care of someone else as their owners go on different missions. What becomes of them afterwards is also unknown.
At one point, Samus saves herself from engulfment by Megaroids via thermal shock by using her Plasma Beam and Ice Beam in tandem. Similarly, near the end of Alien3, Ripley exposes the Runner alien to the heat of the factory's molten lead, and quickly turns on the sprinklers, causing its exoskeleton to rapidly shatter, also via thermal shock.
Aether having a turbulent atmosphere that damages the protagonist's ship and leaves them stranded on the planet is a concept that also appears in Alien, where the Nostromo lands on LV-426 until repairs are complete.
The Splinter hive in the Federation Marine' Ops base and the discovery of the dead troopers caught in webs is similar to the discovery of the Alien hive and cocooned colonists in the colony complex in Aliens as well as in a deleted scene from Alien.
The scene revealing that the Splinters managed to kill off the entire task force is similar to the hive discovery scene in Aliens, which kill all Marines except for Corporal Hicks, Privates Hudson and Vasquez and Lieutenant Gorman, who all later die.
The scene where Dark Samus aims at Samus during their first encounter is stated in the game's storyboard art to reference a scene in Aliens (specifically, the climax where Ripley uses her flame gun to finish off the Queen Alien).
Dark Samus resembles the Alien creature slightly due to her black coloring, skeletal feet and clawed fingers.
The Chykka boss resembles the second stage of the Alien life cycle, the Chestburster.
The character PFC G. Haley is the weakest Marine emotionally, similar to Private Hudson in Aliens. They are both later killed.
The scene where Samus awakes from a nightmare (in which Dark Samus is reborn and is released from an exploding Phazon canister) might have been inspired by another nightmare scene in Aliens (in which a Chestburster erupts out of Ripley while she is in the hospital).
One scene during the invasion of Norion depicts Ghor fighting a Berserker Knight in his armorsuit. This is similar to the climax of Aliens, where Ripley battles the Alien Queen with an exosuit cargo loader.
The Berserker Lord's head strongly resembles that of a Queen Alien.
Later in the game, the other Hunters become corrupted by Phazon and Samus is forced to kill them. This is a recurring element in the Aliens series, in that the protagonists sometimes have to face the choice of killing their comrades because they have been impregnated with a Xenomorph embryo (Ripley killed herself in Alien3 and wanted to kill a surviving Xenomorph host in Alien Resurrection. This theme has also appeared in the spin-offs and crossovers of the franchise).
Samus is the last of the original group of four Bounty Hunters hired by the Federation. In the first and in the beginning of the third Aliens film, Ripley is the sole survivor while her comrades are killed.
In Aliens, Ripley seemingly destroyed the source of all the Xenomorphs in a nuclear explosion. Likewise, Samus destroys the source of all Phazon by causing the planet Phaaze to explode. Additionally, there are numerous Phazon Metroid hives and eggs on the planet. This is similar to the Xenomorph Hive in Aliens.
When out of his armorsuit, Ghor is a gentle person and very compassionate, but his armorsuit notably alters his personality to become more violent. This is similar to Ripley during her cloning in Alien Resurrection, whose enhanced strength also enhanced her violence.
The countdown to the destruction of the Spire Dock is similar to the countdown of the original Alien, in that the female protagonist willingly activates a self-destruct mechanism to accomplish an objective and goes to the escape pod, but is forced to make an unexpected detour before escaping.
The whole concept of Samus picking up a distress call from an abandoned colony, investigating it with a group of Marines, and every member of the Marines being slowly killed off with one soldier, Samus, a survivor of the BOTTLE SHIP and a remnant of another Marine surviving are all similar to the plot of Alien, wherein Ripley's crew is forced by contract to investigate a distress beacon, let a Facehugger on board to attempt and remove it, and eventually everyone except for Ripley is killed. It is also, to a lesser extent, similar to Aliens.
Adam Malkovich is hostile towards Samus for leaving the Federation Army due to "a certain incident". Similarly, in Alien3 the superintendent Harold Andrews believes Ripley to be incredibly disruptive to the status quo in the prison when she crash-lands there. Anthony Higgs in Other M and Leonard Dillon in Alien3 are the only two inhostile toward Samus and Ripley.
Anthony Higgs shares many similarities with Corporal Dwayne Hicks from Aliens. Both of them are the sole surviving soldier from their squad, and share a close bond with the protagonist.
There is a black man in every Alien movie, so Anthony Higgs might have been a reference to this trope.
The "Baby's Cry" coming from the BOTTLE SHIP is like the warning signal from the downed vessel on LV-426 in Alien.
The RB176 Ferrocrusher that Samus battles strongly resembles the loader that Ripley used at the end of Aliens. "Ferro" is also a character in Aliens.
MB's personality as a rogue android is likely inspired by that of Ash in Alien, both have a condescending view of humans.
One of the soldiers (The Deleter) is actually an assassin working for traitors in the Galactic Federation who want to use Metroids as bioweapons. The Deleter tries to kill the whole 07th Platoon, Samus and MB to erase all evidence of the traitors' involvement. This element occurs often in the Alien series; usually in every Alien film there is an individual working for the government in the group of survivors (like Ash in Alien and Carter Burke in Aliens) who intends to recover a Xenomorph and, usually, kill all the other survivors in the process to remove all evidence.
The scene where the Deleter kills K.G. Misawa by throwing him into Lava is similar to the scene of Ripley's death in Alien3.
Samus was used without her knowledge to create bioweapons, using clones of DNA samples extracted from her suit. This mirrors Alien Resurrection quite closely as Ripley was cloned for a similar purpose; for the extraction of a Queen Alien within her body which can reproduce Aliens. In Other M a Queen Metroid is also created, just like Alien Resurrection.
Little birdie's husk, along with the Mystery Creature's, is similar to the way in which an Alien leaves its host, by breaking out of the rib cage. A character also discovers evidence of the creature's metamorphosis into a larger stage through discovery of shed skin in Alien.
The Mystery Creature itself has features that make it similar to the Alien. It has a skeletal, segmented tail and what appear to be vestigial wings similar to the Alien's dorsal fins. It also has green blood, along with Ridley. The fact that the creature is somewhere loose on the BOTTLE SHIP is also similar to the concept of the first film.
The moment where the Mystery Creature assaults a pinned down Samus with it's barbed tail almost exactly mirrors a shot where the Queen Alien uses it's tail to attack Ripley at the end of Aliens.
Samus returning to the BOTTLE SHIP before it is destroyed to recover something important (in her case, Adam's helmet) is similar to Ripley returning to the hive to rescue Newt in Aliens.
Samus escaping with Adam's helmet is also similar to Ripley escaping with Jones, her cat.
Samus has posttraumatic stress disorder, a result of Ridley. This is similar to Ripley being traumatized by the Alien in Aliens. However, both are able to overcome their fears and exterminate their foes.
Before the Brug Mass battle, one of the soldiers says "They're coming out of the walls!" This is also a line from the hive scene in Aliens.
MB and Madeline Bergman flee from Samus out of fear, similar to Newt, another survivor.
Samus discovering Adam was the one credited as the creator of the report for Project Metroid Warriors is similar to Ripley discovering, in Aliens, that Burke ordered the colonists to investigate The Derelict without warning them.
The scene where the Queen Metroid emerges from blast doors is similar to another scene in Aliens, where the Queen Alien exits a lift after being able to operate it.
The Queen Metroid seems to have strong empathetic emotions towards her babies, as she will stomp on the ground and send a harmless shockwave to break through the ice freezing them. She also screams in agony and anguish when six of them are killed. This is similar to the Alien Queen in Aliens, who was extremely protective of her offspring, to the extent that she screamed in rage when Ripley burned her offspring alive when hatching in the sequel.
Ridley has 3 stages in his life cycle, much like Aliens have a three-stage lifecycle excluding the queen: Facehugger, Chestburster and adult form.
The Holographic Generator technology creates an artificial environment. A similar technology is seen in a deleted scene in Aliens.
Sector Zero detaches from the BOTTLE SHIP by having clamps holding it release, before the sector floats off into space and explodes. The Narcissus escape shuttle also does this at the end of Alien.
Samus awakens in a hospital after having nightmares of Mother Brain annihilating the baby, and gives a report, before responding to a distress signal, similar to Ripley in Aliens.
The Zeta Metroid's physical similarities to the Xenomorphs in the original game are further highlighted here, not only having a redesign that is even closer to Xenomorphs than before, but also having its introduction to Samus being taken directly from Alien, where it drools on Samus and then lowers its tail before dropping to the ground.
The Metroid Detector now makes a beeping sound when Samus is close to a Metroid, similar to the Motion Trackers used by characters in the Alien films. The beeping gets slower or faster depending on how close Samus is.