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After defeating the Metroid Queen, Samus learns from the scientist Madeline Bergman, that her AI partner MB was behind the destruction on the Bottle Ship. Realizing that MB was directing the Bottle Ship towards the Galactic Federation HQ to punish the humans for their behavior, Samus and Madeline found MB in the lower reaches of Sector 1. As MB held Samus and Madeline off at gun point, a platoon of Galactic Federation soldiers stormed the room and attacked the rogue AI. MB dispatched an army of creatures to fight off this new threat, leaving Samus to protect Madeline.

As Samus was able to defeat a majority of the creatures, Madeline stepped forth and disabled MB with her own freeze gun. As MB fell back frozen, a mysterious man hidden on the higher level of the room ordered his men to fire on MB. This man was none other than a well respected Colonel from the Galactic Federation who sneaked on board the Bottle Ship with his own soldiers sometime after Adam had detached Sector 0. As he came down to inspect the scene of the confrontation, he smirked at the fallen MB and crushed her hair clip underneath his boot. Noticing Samus, he thanked her for her help, and asked her to leave the Bottle Ship so that his men could control the situation. Samus refused to leave without Madeline, but the Colonel reminded her that with Adam Malkovich dead, Samus was an outsider with no jurisdiction over him. As Samus still refused to leave, he reminded her that her history of transporting illegal cargo could make things very troublesome for her. He called for one of his men to escort Samus to her ship, when he realized that soldier escorting her was not one of his. The soldier revealed himself to be Anthony Higgs, having survived his encounter with Ridley earlier. Anthony kindly informed the Colonel that he was under orders from the Chairman of the Galactic Federation to locate and extract all survivors from the Bottle Ship. The Colonel angrily protested, but knew that he couldn't move against the Chairman, and allowed Anthony to leave with Samus and Madeline.

Prior to Samus's return to the Bottle Ship, the Colonel and his men had the bodies of all the Platoon 07 soldiers, Ridley, and Nightmare removed. It is likely that he was responsible for Ridley and Nightmare being present on the BSL Research Station during the events of Metroid Fusion.

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