Adam Malkovich

Commander Adam Malkovich (アダム・マルコビッチ Adamu Marukobitchi?), previously General Adam Malkovich, was the celebrated military "genius" that served in both the Federation Police (formerly), and in the Galactic Federation Army as the only Commanding Officer to Samus Aran during her time in the Galactic Federation. He was described by Samus as being gruff, harsh, a perfect military mind, and relentless in criticism - but not a machine obsessed with duty. The way he is described suggests that Samus had grudging respect and admiration for him that has since grown into friendship. Adam is first introduced in Samus' soliloquies in Metroid Fusion, though he is seen and interacted with in Fusion's prequel, Metroid: Other M, which greatly expands on his character, revealing that he left the police, and joined the Army as a commander, leading the 07th Platoon.

He is widely hated amongst fans for being kind of a "dick" or "jerk".

Background
During Samus' time with the Federation Police, Adam was the only one who truly understood her; thus, Samus viewed him as her best friend and surrogate father figure. He "joked" around with Samus, saying the phrase "Any objections, lady?" after a briefing. It is said in Fusion it was to denote trust, but in Other M, Samus responded with a "thumbs-down" while the other troopers responded "thumbs-up" as acceptance to the knowledge from the briefing. The reason why Samus responded differently was for two reasons: derision at being called "lady", and understanding of the mission directives.

Later, it was revealed that Adam had a younger brother, Ian, who supposedly died during a mission when Adam sacrificed him to save approximately 300 people on board a cruiser. During that time, Samus protested to save Ian, but Adam ignored her, and ordered to dispatch the malfunctioning drive unit. Whaaaat a dick!

2002 Manga
Malkovich has a small role in a few chapters of Metroid, as a commanding officer who arrives after Samus' first training mission in the Galactic Federation Police. He allows Samus to investigate Zebes for Chozo survivors before the Federation attacks. He also commands the Federation Army Special Ops Battleship Vixin IV which he uses to battle Ridley near the end of the manga in an attempt to give Samus more time to storm Zebes.

Malkovich would call Samus Aran “Lady” during missions, which Samus notes that he managed to make it sound dignified where it would seem sarcastic from anybody else. When giving her orders he would end with “Any objections, Lady?” The question was rhetorical, as he knew she wouldn’t disagree. It was just a phrase to denote their trust.

Other M
During the events of Metroid: Other M, Adam receives the "Baby's Cry" distress call and leads a team of Federation Marines on the BOTTLE SHIP, the Galactic Federation 07th Platoon (this team consists of Anthony Higgs, Lyle Smithsonian, Maurice Favreau, James Pierce and K.G. Misawa). When he sees Samus Aran, he refers to her as an "outsider" on the team, treating her very coldly and ordering his team not to reveal any details of their mission to her. Samus even states that when breaking open a Red Blast Shield, he scowls at her as the Missile was unauthorized. However, he accepts her after they cooperate in defeating the Brug Mass, realizing they need her support, and from then on starts authorizing different items and equipment for Samus to use, at the cost of her completely obeying his orders. Adam is then stationed in the Bottle Ship Control Room. He orders the platoon to different areas of the BOTTLE SHIP and allows them to use whatever they can due to the threat, but their top priority is to locate survivors. He learns that the communication systems of the platoon are rendered useless with the exception of Samus's, which Adam uses to see everything she does. What a creep.

Samus and the platoon (save for Adam, who is still monitoring them like a creep) later rendezvous at the Biosphere Test Area and discover a dead cybernetically enhanced Zebesian. Maurice uncovers that the Galactic Federation has been experimenting with bioweapons, which are strictly prohibited under Galactic Federation law. Samus decides not to press Adam on the matter, knowing he is strongly against the use of bioweapons and other living things for unnecessary purposes, believing that life is not to be tampered with. Because of this, Samus realizes he would have been against her delivering the Baby to the Galactic Federation, and despite her intentions, it was a clear violation of protocol. Shortly afterward, several active Zebesians attack Samus and Adam orders the Platoon to evacuate the building while Samus handles the threat. Prior to fending off the Mystery Creature, Adam orders her to hunt the Mystery Creature down to Pyrosphere, though later suggests that she should look for survivors in Cryosphere. However, when the Mystery Creature becomes more threatening, he tells Samus to hunt for it again and orders her to use the Plasma Beam against it.

After Samus saves Anthony from a Rhedogian, he asks her what she thinks of Adam. Samus reminisces about Adam's brother, Ian, who was responsible for repairing the drive unit of a ship with approximately 300 people on board. The drive suddenly goes critical, and although Samus volunteers to save Ian, Adam refuses to allow her to risk the craft. Instead, he commands the crew to disengage the drive unit before it explodes, sacrificing his younger brother to save everyone else on board. Despite what they thought then, Samus and Anthony realize they might not be alive had Adam not made the decision he did, one that no one should have to make.

Continuing the hunt to the Geothermal Power Plant, the room is shrouded by darkness with the Mystery Creature (who had molted) blazing the area. Adam orders Samus to use her Super Missiles to open a Magma-eruption port, pouring Lava which lights the room. The evolved creature turns out to be Samus' nemesis Ridley, thought to be destroyed along with Zebes, much to her horror and shock. Realizing Samus is unable to respond, Adam tries to get through to her and commands her to use the Plasma Beam before he is attacked by someone who shoots off his comm earphone. After defeating her old foe, Samus realizes that she has been unable to contact Adam since. She arrives at the conclusion that Adam may have been well aware of everything that was occurring on the BOTTLE SHIP before he even arrived, making him the biggest threat in the Deleter's eyes. Although Adam would not go down easily and may have learned about the assassin, she believed his life was in danger. Pursuing the possible traitor to the Biosphere, after he deactivates a bridge and destroys the controls to hinder her progress, Samus "objects" Adam by activating her Space Jump and Screw Attack which leads her to the Bioweapon Research Center while flipping about, giving Adam both middle fingers and blaring dubstep at high volumes.

Expecting to find the assassin, Samus instead encounters the woman she encountered earlier, claiming herself to be Madeline Bergman, the person in charge of the bioweapon project. She explains the Galactic Federation's plans to create an army modeled after the Space Pirates after the destruction of Zebes, which included Metroids, the Zebesians, and an A.I. based on Mother Brain called MB. She also reveals that Adam was the one who authorized the project. Samus decides to head into Sector Zero to destroy the Metroids and MB.

As Samus encounters an Infant Metroid at the entrance of Sector Zero, Adam shoots her in the back with what looks to be a freeze gun that disables her Varia Suit, before shooting the Metroid with his freeze gun. When Samus regains consciousness, he explains to her that he did this to prevent her from entering Sector Zero, which contains Metroids that could not be frozen, and that Samus is incapable of destroying. Developing bioweapons with their obvious weaknesses intact would be suicide, so the Sector Zero Metroids had their weakness to cold removed through genetic engineering. Pressing him on why he was credited as the creator of the Metroid military program report, Adam explains that he was requested by Galactic Federation HQ to write a report in which he outlined the potential dangers of such a program. Although HQ listened, a small group within the Federation co-opted his report for their own purposes, which allowed the scientists to proceed with the project.

Realizing the threat of the Metroids, believing that their extinction was wise, and the threat of MB planning to attack the Galactic Federation, he decides to enter Sector Zero and destroy it by himself. By inflicting enough damage to the sector, it would detach from the BOTTLE SHIP before self-destructing, which would ultimately destroy the Metroids and MB, at the cost of his own life. He also gives Samus several orders; stop the BOTTLE SHIP's intercept course with the Galactic Federation, secure a survivor he located in Room MW, found in the Bioweapon Research Center, and destroy Ridley. He also warns her that the woman she met earlier was no ally. Samus refuses to allow this and volunteers herself to destroy Sector Zero, much like the incident involving Ian, but Adam claims that he cannot defeat Ridley, and he is not the galactic savior like she is, but is merely human, and can at least save her. After apologizing to Samus for getting a little rough with her, he leaves her behind. She is unable to stop him in her weakened condition, and he locks the doors to Sector Zero. His last words to Samus are "No objections, right Lady?" to which she responds with a bitter thumbs down. He then exploded and everyone died. Yay!!!

Metroid Fusion
During her mission at the BSL research station, Samus is given a personal computer to serve as her new Commanding Officer. The computer reminds her of her former CO so she decides (with noted irony) to name it after Adam.

At the end of Metroid Fusion, when the ship's computer Adam informs Samus that the Galactic Federation will soon be landing aboard the Biologic Space Laboratories research station to try and capture the SA-X to use it for military purposes, Samus questions the orders and accidentally calls the computer Adam. This leads to a conversation where Samus realizes that somehow (the computer says, "any objections lady?" after giving her an order to crash the station), the computer is the real Adam Malkovich. With the computer's identity established, it decides to help Samus and agrees with her about the X threat. The two of them conspire a means to destroy the research station, and catch the planet SR388 in the ensuing vaporization field, and hopefully destroy the X threat for good.

It is then that Samus learns that it is a common practice to upload the minds of great leaders and scientists into computer form, and this is evidently what happened with Adam Malkovich and Samus's new gunship. The pair set off for an unknown destination.

The Adam computer is housed in the onboard computer in Samus's new Gunship and can be contacted through the Navigation Rooms. The computer has some control over the station, though it is limited to opening/locking doors and restoring power to elevators. Unusually, it has a single purple eye that seems to serve as its face.

Also, right before the computer gives Samus the order to blow up the station, it (possibly under the influence of its Galactic Federation components) gloats and tells Samus "when Adam chose who would live, he chose incorrectly", referencing Adam's sacrifice of his own life to save Samus'. Up until the point when Samus realises the computer's identity, it seems to be under the influence of these components, as it is aware of the presence of the Restricted Lab but chooses not to tell her. Additionally, as seen in dialogue with the Incoming Dispatch, it seems to have been chosen to keep Samus in the dark regarding the Federation's plans for the Metroids and the X.

Appearances in Fanon
None yet, but let's be honest here, not many people are going to be adding him anyway.

Trivia

 * The "eye" of the Adam computer bears an uncanny resemblance to that of HAL 9000, the infamous computer in Stanley Kubrick's film 2001: A Space Odyssey. HAL also serves a similar purpose as onboard computer, though he has considerably more control over his own ship than Adam (the entire ship, in fact). The ending, where Adam locks Samus in a room, is also similar to the famous scene from the film where HAL locks David Bowman out of the spaceship Discovery One, even down to their dialogue.
 * Adam's computer form may have been based on the android Bishop 341-B from Aliens. Like Samus, Ellen Ripley distrusts Bishop due to her encounters with the android Ash in Alien, but eventually comes to accept and trust him. Like Adam, Bishop "dies" and becomes an adversary to Ripley in Alien3.
 * Adam's actions toward Samus in Other M are also similar to that of the prison warden Harold Andrews in Alien3, who disapproves of Ripley.
 * In Other M, if Samus delays in the Bottle Ship Control Room after being ordered to follow Lyle to Sector 1 / Biosphere, Adam asks her what is wrong and reminds her to head to her designed destination. The same applies if she tries to enter a sector that she isn't assigned to (even though it is actually locked) at the Main Elevator.
 * "What's wrong? Head to Sector 1/3."
 * In Other M, Samus references Adam's catchphrase by asking, "Any objections, Adam?" when she triggers her Space Jump and Screw Attack without his official consent.
 * Interestingly enough, Adam knows nearly all the events of Other M prior to the Metroid breeding program, yet he never mentioned one word of it to the 07th Platoon or Samus. This what some people call a plot hole, but Other M doesn't have a plot!
 * In Other M, when Samus is killed in some points, Adam will yell her name and then order her to respond. This may be possibly be a deliberate reference to the Metal Gear series, where Snake's or Raiden's name is shouted in a similar manner on their game over scenes. However this might not be, as Other M isn't smart enough to function as a game.
 * When Adam sacrifices himself to destroy Sector Zero, the light in the background gives off a halo of light around him, when aimed correctly, which represents his upcoming sacrifice. Examples of this halo include portrayals of Mary in many medieval paintings, and Bill in the "Sacrifice" poster from Left 4 Dead. However, in a later interview, this was revealed to be a mistake and Adam was intended to have a pink background with pink ponies prancing around as he died, with the song "The Witch Is Dead!" from the Wizard of Oz.
 * Adam is one of two people to have acted as a surrogate father to Samus, the other being Gray Voice, whose blood was given to Samus.
 * In Other M, the cutscene where Samus reaches her ship at the end of the game features an eye-like object resembling the eye of the Adam computer in Fusion.

And them's the facts!