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. The only information available about Adam is from Samus’ own words and depictions of him. He is described 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. The first reference to Adam was from Samus' soliloquies in Metroid Fusion.

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.

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.

It is known that Adam sacrificed his own life to save Samus. Given that he is alive during the events of Metroid: Other M, it is known that he survived his battle with Ridley's forces during the course of the manga.

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. However, he accepts her after she defeats an unknown purple creature. There is much speculation that Adam's fate will be revealed in this game. After the seventh trailer, it is speculated he died facing ULF 46.

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's.

Trivia

 * The "eye" of the Adam computer bears an uncanny resemblence 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 Odyssey, even down to their dialogue.
 * If the Metroid series was inspired by the Alien film series as speculated, 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).