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.
