Aliens are the primary antagonists of the Contra series. Throughout most of the games, it was believed that they, along with their army Red Falcon, were extraterrestrial invaders seeking to conquer planet Earth, but the events of Contra: Shattered Soldier revealed they are in fact part of a highly sophisticated, organic defense system programmed to protect their creators' treasured Moirai Relic. They are heavily inspired by H. R. Giger's Necronom IV, which is also the basis for the xenomorphs from the Alien film series. Their cells are used by human antagonists in later games for their own purposes.
As previously mentioned, the "alien" antagonists featured in the games are artificial lifeforms, forming as a part of some sort of security system created by an unseen race of omniscient aliens to protect their sacred technology. Their creators ruled the galaxy prior to the existence of humans, but have long since ascended to a higher plane of existence and left behind their ruins across the cosmos, one of which was a sanctuary located on Jupiter. The sanctuary was discovered by the Earth Federation Government and after thorough investigations, they obtained the immensely powerful and mysterious Moirai Relic and brought it back to Earth for scientific research and analysis. It was this very act that prompted the activation of the Red Falcon army, leaving Jupiter and reaching Earth multiple times in order to aggressively retrieve the relic.
The Triumvirate falsely led the public to believe that Red Falcon were alien invaders in order to hide the truth. With this false belief motivating Bill Rizer and Lance Bean, they successfully managed to stop the "alien invaders" at completing their mission throughout the years.
The aliens are presented in all shapes and sizes in every game, usually possessing hideous, monstrous appearances, with some possessing insectoid, arachnid, crustacean-like traits or other animal features. Disturbingly, some alien organisms share traits very similar to humans, such as faces. Most are hostile to humans; while there are very few that are harmless, this is mostly due to them being part of their original environment (such as organic walls in the background). Several games hint that every bit of alien matter, such as the various organic hives and every alien creature seen throughout the series, are born from a highly adaptive, rapidly multiplying cell. This would make the cell that creates all alien mass akin to a stem cell, due to its capacity to differentiate into many specialized forms with roles assigned to them. The alien creatures' various and inconsistent forms may result of the progenitor cell(s) continuously adapting. However, some notable entities, like Java or other bosses, are recreated with little to no change.
Many alien types are capable of shooting out of their bodies all sorts of energy-based projectiles as an offensive ability. There are some types who launch or shoot out organic weapons such as spikes or smaller parasitic alien life forms at their enemies. Others lack the capability to create any long-range weapon whatsoever, and instead rely on physical attacks only or technology as an alternative.
The alien armies do not solely consist of creatures born directly from alien cells; there are also humans, mutants, and robots which make up large portions of their forces. The humans that have willingly or unwillingly allied with the aliens are usually presented in the form of soldiers and are often the first and weakest enemies the player has to deal with. Mutants are creatures resulting from humans or animals being converted into alien-like monsters via direct infection/exposure to alien matter or through the use of technology under the guidance of alien and/or human factions. The origins of the robots are ambiguous, as they could either be results from human-based technology or from the aliens using their own technology to create and develop them.
The aliens' first attempt at finding and retrieving the Moirai Relic began when a meteorite landed on the ocean near the Galuga Island. Two years later, the Red Falcon army was established on the island and they began attacking humanity. Bill Rizer and Lance Bean are sent into their headquarters where they fight mostly human soldiers and security robots. The first alien creature encountered in the game is the boss of the waterfall stage, which is seemingly merged with the gate leading to the second military base and is capable of attacking with tentacle-like limbs and projectiles launched from its mouth. In the arcade version of the game, this gate is seemingly composed of two alien-like entities merged together which attack strictly with mounted turrets; due to their metallic-like appearances, this rendition of the waterfall boss may possibly be a robotic creation. Afterwards, aliens do not reappear until the final stage: The Lair.
The meteorite presumably carried alien mass that would form into Red Falcon's lair and its inhabitants. The lair was an underground cavern completely overrun with pulsing organic matter, all of which was fed by the giant beating heart found at the very end. The first hostile alien encountered here is the Para-slug, which spat out an infinite supply of flying grub or shrimp-like creatures that are possibly its own young offspring. Located deeper in the hive were mouths that shoot out homing projectiles, eggs which continuously spawned spider-like creatures and finally, the giant heart itself. In the Famicom version of the game, the entire hive pulsated along with the heart and as the latter received damage, the pulsations of both the surrounding area and the organ itself grew faster. As the heart died, the entire hive ceased all movement, indicating the death of the area.
Their second attempt involved taking over a United States Army base but the Database of Contra: Shattered Soldier reveals that this Army base is located at South America. Many of the enemies in the first few stages are human soldiers under the mind control of the aliens. Contrary to the first game, the aliens here are far more prominent, as the stages become more and more infested with them the closer players get to Red Falcon's new headquarters. In the arcade version of the game, the hive is divided into the last two stages, with the boss guarding the entrance to the first one consisting of a seemingly organic alien tower. The aliens consist of runners (which become a staple in subsequent games' hive stages), eggs with shrimp creatures, a large winged cycloptic alien, giant floor mouths that attempt to consume the player, among others. The final boss of the game is Gyaba/Jagger Froid, who in Contra 4 (the second to last game to be released) would be relabeled as the Red Falcon leader itself. He is located within the second hive stage and carries an embryo inside its forehead that grows wings and flies off after Bill and Lance kill Gyaba. The fate of this alien embryo is never revealed, though it is possible it grew into the new Gyaba that appears at the end of Contra III.
In the console versions of Super Contra, Gyaba is the third to last boss, with two additional hive stages found beyond him. The final boss there is instead the frog-like Kimkoh and the earlier mentioned alien tower (which served as a boss prior to the first hive in the arcade version) became the second to last boss with a more emphasized biomechanical design.
The plot in the Japanese version states that an alien cell is being researched and exploited by an unnamed hostile nation seeking to produce weapons with it, with Bill Rizer being sent in to stop their operations. The North American version however describes that the hostile nation is working for the alien cell itself, the latter which has been given the name Black Viper (following the naming theme of Red Falcon). Neither version of the game sheds light on where or how the alien cell/Black Viper came into contact with the nation, but it can possibly be assumed to be part of Jupiter's security system with the intent of retrieving the Moirai Relic. In fact, Contra 4 states Black Viper to be a sibling of Red Falcon.
The aliens appear in Area 4 and 5, the last two stages of the game. Unlike prior games, the final stage is not a hive, but it is instead a research lab filled with human soldiers along with spider-like aliens bursting out of their containment tubes. The final boss is an advanced mech robot that protects the room containing the defenseless Black Viper Cell. The hive is visited in Area 4, inhabited by many crustacean and arachnid-like aliens, which presumably originated from the alien cell. The later released Contra 4 retcons the events of this game, stating that Black Viper was killed by two other heroes named Mad Dog and Scorpion.
The aliens and their leader come back in the year 2636 with a vengeance: they bomb an entire city to mark their arrival. The scale of their "invasion" is far larger than prior games, spanning across various regions instead of an island or military base. Also, aliens appear in every level, either serving as a boss or a standard enemy type.
The game's final level is once again an organic hive, with the entrance serving as the prior stage's boss (a dome-like alien with an eyeball at the top). The hive's most common inhabitants are runners and wall mouths that spit out homing projectiles. Also featured here are many minibosses, all of which are notable entities from prior games: the Para-Slug with its spawning grubs, the giant beating heart with its spider-laying eggs, Kimkoh and the large winged cycloptic alien.
Interesting to note is that the giant heart's destruction did not trigger the death of the hive, which was the case in the first game. It would seem that Red Falcon (previously known as Gyaba/Jagger Froid) is capable of keeping the hive alive without the massive heart. It is only with his defeat that the area begins to collapse. Red Falcon has two all new forms compared to his predecessor, consisting of his own massive one-eyed brain and a four-limbed armored form.
Black Viper returns with an alien army, prolonging the Alien Wars by destroying a massive city in a similar manner that her brother, Red Falcon, did in the third game. Two years following her return, she had recruited many humanoids and aliens to her cause, along with creating mutants in laboratories and various robot factories. While she remained in the ruined city, her minions have spread out and overrun many surrounding landscapes.
The first appearance of alien matter is seen in the first boss of the game, inside the defense gate a brain-like organ is featured as a power source capable of firing beams. A large alien serves as the boss of the second stage, and afterwards they are absent until the fifth stage where the aliens are strictly aquatic, though they may simply be mutated/infected fish as well. Once reaching the destroyed city, alien activity is seen in the form of gray grubs, man-faced mutant dogs, creatures with insect-wings and a massive, incredibly fast pill bug-like entity that serves as the stage's boss. Other than its throbbing organs which harm players if they touch them, the boss has no offensive abilities of its own and relies entirely on armed, vehicle-riding robots to defend it. The boss is eventually killed and collapses in front of the entrance to this game's organic hive. Interesting to note is the presence of human beings within the pill bug boss' pulsing organs, suggesting that it was carrying either live or dead cargo inside it with the intention of bringing it to the hive or beyond it.
The alien hive is vastly smaller and simpler than those in the past. The inhabitants are runners, spiders and eyeballs which serve as sentries and gate-locks. There are also large mouths on the walls, but they are completely harmless. The boss of this area is a giant beating heart protected by infinitely spawning eyeball sentries.
Similar to Operation C, there is a stage beyond the hive, named "Harvest Yard" and it is the final area of the game. The players walk upon an underground dumping site, likely beneath the city, where thousands of human corpses are being piled up in the background; it is possible that the pill bug boss was intending to carry its cargo of human corpses to this area. A large containment tube is eventually located with a radically transformed Black Viper inside. She immediately breaks out and begins attacking with her new praying mantis-like form, but shortly begins to absorb the nearby bodies and falls into the massive pile. She emerges as a floating giant and players enter her body through her rear by destroying the tip of her abdomen. Her insides have grown to the point of becoming a literal alien hive heavily infested and defended with runners, winged flyers, spider-laying eggs and large mouths which spit homing projectiles; these aspects make Black Viper's interior more faithful to previous games' hives. The inside of her skull contains a smaller Black Viper with a body reminiscent of her brother Red Falcon's from Contra III, including a cycloptic brain. Destroying the brain results in the destruction of the giant Black Viper, who by this point had reached high above the atmosphere.
Black Viper's body transforming into a hive-like area and the appearance of the organism inside her skull may imply that Red Falcon himself had gone through a similar process to create Contra III's hive and final boss.
At the end of the Alien Wars triggered by Red Falcon and Black Viper, an alien cell was recovered and kept under heavy surveillance by the government. For five years, Earth saw no alien-related conflicts until the appearance of the renegade Colonel Bahamut. With the aid of his accomplice Dr. Geo Mandrake, he stole the cell with the intention of using it to create a weapon capable of overthrowing Earth's ruling governments. The main characters Ray Poward, Sheena Etranzi, Brad Fang and Browny are tasked with several missions in order to stop his plans. Depending on the decisions and paths chosen by the characters, the Alien Cell is used in different ways by the antagonists.
- In one path, Bahamut's team has enough time to work on the Alien Cell and have it grow into Big Magnum, a cyborg alien brain powering up a satellite weapon of mass destruction. With Bahamut at the cockpit connected directly to the alien, he succeeds in bombing a country. The battle against him and Big Magnum consists of damaging the cockpit as it attacks with a variety of unusual beam patterns. Prior to this final battle, Geo Mandrake transforms most of Bahamut's men into squid-like mutants; these may be the results of his extensive experiments with the Alien Cell. The ending to this path sees the destruction of the entire weapon and the deaths of Bahamut along with the heroes.
- In a second path, the heroes arrive at a facility in the woods where brown aliens created from experiments with the Cell are kept in stasis tanks. They are in various stages of development, and those fully grown break out to attack players. As they reach one of the higher floors, Bahamut is seen transforming Dr. Mandrake into a mutant as punishment for the damages his experiments have done (most likely the brown aliens). After the heroes kill Mandrake and reach Bahamut, the latter reveals that research on the Cell has provided him with the means of fusing with it and becoming the Ultimate Being, resulting in a tall, muscular and hairless brown humanoid capable of super speed, flight and unleashing energy beams. However, damaging Bahamut causes him to lose control of his newfound power, mutating him into a horrendous two-headed beast possessing features from the first and final bosses of Contra III. Further damage results in a third and last mutation: a small alien heart protected by numerous heads resembling Bahamut's first transformation. Bahamut's death causes the self-destruction of the facility, with the heroes leaving the vicinity on a vehicle. The earlier brown aliens share a strong resemblance to Bahamut's first form during the battle, suggesting the former were prototypes to the Ultimate Being.
- A third path consists of an early death of Dr. Mandrake, the lead scientist in Bahamut's research on the Alien Cell. This buys the heroes enough time to reach the Colonel before the Cell is fully utilized, resulting in a fight against a fully human Bahamut. Upon defeat he reveals that he placed the unstable Alien Cell in a missile warhead destined to fly into the atmosphere and spread the Alien contagion around the globe. As players manage to climb on the side of the warhead mid flight, numerous alien organisms begin breaching the hull of the missile due to the rapidly multiplying cell within. These include slug-like creatures, a large worm which spews out flying insectoids, and at the tip of the missile is an alien centipede capable of firing energy beams. The death of the centipede reveals the warhead's payload: the Alien Cell, now grown into a monstrous purple alien consisting of disfigured faces with pained expressions and misplaced organs. It attacks players with rapidly regenerated arms, but destroying them repeatedly will cause one of his heads to stretch out and vomit numerous maggots. This same head contains a red vascularized organ in its throat, possibly an alien heart that keeps the entire entity alive. Sufficient damage will kill the boss and destroy the missile. The heroes are rescued by a small plane.
- The 4th path provides the most insight about the Alien Cell's abilities. The death of Dr. Mandrake causes Bahamut's plans to be stalled, allowing the heroes to catch him off guard as one of his soldiers rushes in to inform that the Alien Cell has broken loose, causing destruction inside their headquarters. Bahamut expresses regret working on the Cell without the doctor's expertise and runs off. The heroes walk into a horrendous sight: a spreading alien mass is slowly taking over the headquarters and converting it into a hive similar to those seen in the past. Containers and engines in the background are being replaced with organs and blinking eyes while the floor panels are being covered by soft membranes and armored tissue. Soldiers are seen on their hands and knees in pain before violently mutating into fast ostrich-like runners that cannibalize on each other. Deeper in the hive are the iconic mouths with their homing projectiles, along with spiders and creatures resembling T-Rex skulls that devour the occasionally spiders. Notable entities such as Para Slug and two Kimkohs are present, though their appearances are drastically altered from their prior incarnations. At the end of the hive is a reborn Red Falcon, now possessing a female human's face, though it eventually changes into the more familiar visage after dealing a set amount of damage. Further damage will cause Red Falcon to expand and reveal a giant alien heart protected by two floating eyeballs. Destroying it will end the battle and cease the expansion of the hive, with Bahamut fleeing the scene in a helicopter.
The above path implies that a single Alien Cell carries all the genetic information necessary to multiply and create not only a hive, but also to recreate or resurrect an entire alien army and its leader, Red Falcon or the Mother Alien. The unnatural cannibalistic behavior of some aliens, along with the vastly different appearances of important bosses, may all be a consequence of Bahamut and his men tampering with the Cell. Interesting to note is that in all 4 paths, the heroes are required to traverse a jungle filled with mysterious creatures: large dragonflies, tall spitting flowers, rolling poly-like insects, savage humanoids and an organic-looking miniboss hiding behind a waterfall. It is unknown if these entities originated from experiments on the Alien Cell or if they are a natural occurrence in the world of the Contra series. A fifth path leading to a joke ending very early in the game has the main characters fight in an underground ring against various bizarre monsters; their origins or possible relations to the Alien Cell are also a mystery.
Taking place 6 years after the previous game, Bill Rizer and Lucia are given the task of fighting a terrorist group calling itself "Blood Falcon", an obvious homage to the alien-based Red Falcon organization of prior incidents. Like Bahamut from Contra Hard Corps, the terrorists are seeking to overthrow the ruling government (controlled by the Triumvirate). The aliens are being used as weapons deployed by the human-based Blood Falcon; some of the terrorists' machinery is powered up by ambiguously organic mass, possibly of alien origin. It is unclear where these aliens came from, though some possible clues are explored later on.
It is eventually revealed that the leader of Blood Falcon is Bill Rizer's old partner Lance Bean, who was thought to have died 5 years ago. During his boss battle in his command center on Galuga Island (Blood Falcon's headquarters), he is shown to possess superhuman abilities and energy-producing attacks, not unlike Bahamut's Ultimate Being incarnation. Further parallels to the Colonel is the origin of Lance Bean's powers: at some point in the last half-decade, he fused with an Alien Cell. When Lance Bean is nearing defeat, he flashes brightly and the main characters find themselves within a hive where they are pitted against five powerful alien organisms. Each one they kill teleports them to another location in the hive for their next fight.
- Their first target is a large alien heart covered with green eyes that exhume smoke. Its only defenses are nearby eggs with constantly release crawlers.
- An elongated worm-like creature as their second target, who tries to cover fill up the entire room with its body in an attempt to attack Bill and Lucia with its head.
- The third battle is against two Kimkohs. Their attack patterns bear similarities with the dual Kimkohs from Contra Hard Corps, however they visually resemble their predecessor from the Alien Wars.
- Their fourth enemy is a segmented alien with a red core in the middle. It attacks with several projectiles.
- The final opponent is Red Falcon himself. Contrary to previous battles in the series, he attacks from below, with Bill and Lucia hanging onto horizontal bones. After Red Falcon's defeat, the players proceed through the rest of the game without fighting anymore creatures related to the alien invaders that have acted as the series antagonists.
A bright flash of white brings the heroes back to Lance Bean's command center, now dying on the floor. He reveals the truth about the Moirai Relic, the alien invaders' origins as an artificial security system created by unimaginably advanced beings to protect their ruins, and the Triumvirate's involvement in the theft of the Relic from Jupiter and its subsequent coverup which triggered the numerous wars and bloodshed against the alien security system. With this knowledge, Bill and Lucia go off to face the Triumvirate who, after years of analyzing the Moirai Relic, believe they have finally tapped into its special properties in order to evolve into god-like beings. However, something goes wrong and in a panic, the Triumvirate are now gone and they could probably merged into a tall, toned white humanoid being, who acts as the game's final boss. The Moirai Relic is seemingly destroyed in the battle.
This boss has no direct relation to the alien invaders and is a result of the misuse of the Moirai Relic. Based on the fact that Lance Bean merged with an alien cell years ago, the various aliens used by Blood Falcon may have originated from that same cell prior or after the merge. The Alien hive battles that took place after the fight with Lance are left ambiguous: it is never clarified if the heroes were teleported inside his body, inside the Alien Cell itself or in a pocket dimension where the Aliens were waiting for them. Whatever the case may be, it can be assumed that the beings encountered in the hive would have eventually made their way into the outside world if Lance wasn't stopped in time.
Taking place almost 2000 years after Contra: Shattered Soldier, plentiful aliens still remain on Earth which has been converted into a prison planet. However, the aliens are no longer viewed as a major threat by the general population. Though never confirmed, It would seem that the destruction of the Moirai Relic has removed the aliens' primary programming and they now roam aimlessly, similar to wild animals. The main threat at this point in time are the Elite Four of Neo Contra and their leader, Master Contra, who's members use the occasional alien organism as weapon, some of which are incarnations of past entities. The heroes tasked with stopping Neo Contra are Bill Rizer, who was recently released from a cryogenic sleep after nearly 2 millennia, and his partner Genbei "Jaguar" Yagyu.
Near the game's end within Master Contra's Headquarters, the main characters stumble upon a heavily mutilated Uranian Devil Gava inside of a capsule. Kept alive via technological life-support systems by Neo Contra, presumably for miscellaneous experiments and as a potential weapon, the alien attacks the heroes from within his capsule. His smaller heads have been severed from his main body and attack from within their own individual capsules as well, and there appears to be four heads. Gava and his minions mainly fire energy projectiles from mechanisms that are installed on their capsules. After receiving sufficient damage, Red Falcon's body breaks down and Searle, his cycloptic brain is unleashed, which roams freely outside of the capsule to attack with its own natural abilities. Eventually, he is defeated, marking the definitive end of the once feared Red Falcon.
It is unknown what happens to the remaining aliens on Earth following the end of Neo Contra. It is safe to assume that the last millennia allowed them to adapt to the planet and will continue to live on it with ease for years to come.