Commander Adam Malkovich

Commander Adam Malkovich (previously General Adam Malkovich) was the celebrated military genius that served as the only Commanding Officer to Samus Aran during her time in the Galactic Federation. He is described by Samus as being gruff, harsh, a perfect military mind, relentless in criticism, but not a machine obsessed with duty. The way he is described suggests that Samus had begrudging respect and admiration for him that has since grown. Adam is first introduced in Samus' soliloquies in Metroid Fusion, though he is seen and interacted with in Metroid: Other M, which greatly expands on his character.

Biography
Adam was Samus' best friend and father figure, as he was the only one who understood her the most. 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 to 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: Denial of being called "lady", and there are no objections.

Later, it was revealed that Adam had a brother, Ian, who supposedly died during a mission when Adam sacrificed him to save approximately 300 people onboard a cruiser. During that time, Samus protested to save Ian, but Adam ignored her, and ordered to dispatch the cruiser.

Metroid (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 pilots 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.

Metroid: Other M
During Nintendo's E3 Press Conference in 2009, the trailer for Metroid: Other M showed Malkovich briefly. His voice is heard for the first time, speaking his famous line, "Any objections, Lady?". He 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), and refers to Samus Aran 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 she defeats the Brug Mass, realizing they need her support, and from then on starts authorizing different items for Samus to use, at the cost of her completely obeying his orders.

Near midpoint, he was attacked by someone (possibly the Deleter), and was temporarily unable to contact Samus. Later, Samus "objects" him by activating her Space Jump and Screw Attack.

Near the end of the game, Adam shoots Samus who gazes at an Infant Metroid and then destroys the creature. He intended to shoot Samus in order to weaken her to stop her from getting into Sector Zero, as Adam attempted to destroy the area by detaching it from the Bottle Ship, which would ultimately destroy both the species and him. Samus declines, but Adam ignores her, and performs the action.

Before he dies, Samus is tasked to head to Room MW to stop an intercept course with the Bottle Ship and the Galactic Federation and destroy Ridley, and not to trust Madeline Bergman (who was initially MB at this point). When Samus declined, he stated that Samus might die due to fighting unfreezable Metroids, and he couldn't kill Ridley since she had more fighting experience than him. Last words before death: "No objections, right Lady?"

It is revealed that the Metroid breeding project on the Bottle Ship was codenamed "Adam Malkovich", yet he wasn't actually involved. The real Adam states he was questioned to sign his name for the project. Adam refused, telling HQ how dangerous it was as they listened. However, scientists co-signed it, which allowed them to continue the project.

In the game's ending, Samus returns to the Bottle Ship to retrieve Adam's helmet. A cutscene shows that when Samus was talking to MB, he saw this and immediately ran to Sector Zero, leaving the helmet.

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 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'.

Adam Malkovich
"Samus' former superior officer, Commander Malkovich is firm and steadfast in his resolve on the battlefield. Beneath this tough exterior lies a strong moral compass, and a deep respect for those that serve him."

Adam Malkovich in Combat Armor
"I hadn't seen Adam since I left the Galactic Federation Army, and seeing him in full battle dress was disconcerting to say the least. He and his team had been called to the Bottle Ship by the same distress call that I followed, and though he clearly wasn't pleased to see me, I decided to stay for the safety of his team."

General Adam Malkovich
"A general in the Galactic Federation Army, he was not only a trusted confidant but also my former superior officer. Because I was so young when I lost both of my parents, there's no question I saw Adam as a sort of father figure. When I rebelled against him, I knew I could get away with it."

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 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. He disapproves of Ripley and believes that the death of Thomas Murphy, the janitor, was due to him being distracted by thoughts of her (all prisoners embraced a religion forbidding sexual relations, which was threatened by Ripley's presence).


 * In Metroid: Other M, Samus spoofs Adam's catch phrase by asking, "Any objections, Adam?" when she triggers her Space Jump and Screw Attack against his orders.
 * Interestingly enough, Adam knows nearly all the events of Other M prior of the Metroid breeding program, yet he never mentioned one word of it to 07th Platoon nor Samus.
 * In Other M, when Samus is defeated in some points, Adam will yell her name and then tell her to respond. This could have been a reference to Super Smash Bros. Brawl when Snake was defeated in Shadow Moses Island prior to being contacted by his allies.