Upon arriving on the Bottle Ship, Samus bumps into a Galactic Federation platoon led by Adam and agrees to aid in their investigation. Shortly thereafter, the soldiers start getting picked off one by one. Samus arrives at the conclusion that one member of the team is an assassin hired by the Federation to silence any witnesses. She dubs this rouge agent the "Deleter" and vows to prevent further sabotage.
Then the thread is dropped entirely.
At some point, the Deleter is himself murdered, but the event is treated with such disregard that I question whether the whole mess was ever relevant to begin with. The game never reveals the identity of the Deleter, and following a case of false accusation against her long-time friend Anthony Higgs, Samus never brings up the subject again. The game continues, the game ends, and that is that.
Significant attention was initially directed towards this development, implying that this character's actions would have serious repercussions later in the game. Not only does he not have any influence aside from a few dead NPCs who might as well have been wearing red shirts, but we also don't even get the satisfaction of a proper unmasking. There are clues that point to James Pierce being the Deleter, but does it really matter?
This is the kind of OCD misdirection that you'd find in an episode of Lost. The director introduces a plot device and convinces the audience that it's important, gets distracted by a flock of geese outside his window, then forgets to plan an adequate follow-up.