A Commanding Officer, or CO, is the commander of a battalion of Federation Marines. They lead their fellow soldiers into battle and possess ultimate authority over their unit, dictating, among other things, weapon and equipment authorization. Some COs are not human, but AI within gunships. Soldiers under their command interface with them through their gunship and via Navigation Rooms. These COs are actually the consciousness of deceased Galactic Federation commanders, uploaded to computers before their deaths, to ensure that their military wisdom would live on. However, as the Federation has shown signs of corruption, it is likely that some artificial COs are manipulated to better suit the Federation's interests by not remembering who they were and protecting illegal bioweapon-related projects conducted by the Federation in secret.

Adam Malkovich was a Commanding Officer to Samus Aran in life and death. She served under him as a member of the Federation Army, as an honorary member of his 07th Platoon on the BOTTLE SHIP and on the Biologic Space Laboratories research station as an AI. Samus compared the artificial Adam to the real Adam, unaware that it was him. As it was unaware of this fact, it concealed the existence of the Restricted Laboratory from Samus and the Federation's desire for the X Parasite. After Samus accidentally called the computer Adam, it remembered its identity and assisted Samus in destroying the BSL and escaping.

Captain A.C. Exeter was the Commanding Officer of GFMC Task Force Herakles.

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