Beware, contains over analytical rambling! Oh, and spoilers.
Samus is no stranger to mystery.
Many of her adventures have placed her in situations where something nasty has obviously gone down and she has to use her deductive resourcefulness to quickly piece together the facts. While not explained in so many words, these mysteries often leave the player to figure things out. Some of these are subtle details that become obvious with a little logic, such as the crashed frigate in Metroid Prime being the same vessel Samus explored at the beginning of the game. Piecing together Ridley's continual cloning and rebirth is such a complex topic, on the other hand, that one could write their thesis on the reptilian Pirate leader.
Metroid Other M is arguably the most plot-driven game in the series thus far, and contains quite a few mysteries of its own to uncover. However, one plot point in particular fizzles out suddenly when more important facts come to light. Assuming all you readers out there have finished the game already, you'll know all the shady shenanigans the Galactic Federation was involved in aboard the Bottle Ship. In order to keep their plans from leaking to the public, they placed a spy on Adam's team of marines — someone to stop anyone from finding the truth, or permanently silence those who do. As the members of Adam's team disappear one by one, Samus figures out about the traitor, and names this person the Deleter.
While the mystery of the Deleter never gets any explanation or closure, and ultimately loses relevance in light of the facts revealed later (not to mention how only one marine survives the whole ordeal), it is still possible to piece the clues together and find out who it was, for curiosity's sake.

Ice to see you.
In the events of Other M, Adam Malkovich's 07th Platoon consisted of six members; Adam himself, Samus' old commander from her days in the Galactic Federation; Anthony Higgs; Lyle Smithsonian; Maurice Favreau; James Pierce; and K.G. Misawa.
As you follow along the game's storyline, things play out something like this:
- Samus receives the call to the Bottle Ship and meets up with Adam's platoon.
- With a temporary cooperation with the group formed, Samus begins her investigation.
- Upon entering the Exam Center, James is found using a computer terminal. As the others arrive, the computer malfunctions and some suspicious data is lost. The team attempts to fix it while Samus explores deeper and discovers the Space Pirate clones.
- Samus heads outside with the marines to fight off an attack from an evolved Little Birdie.
- Lyle is found dead outside the Biosphere Test Area with what looks like a blaster wound. Little Birdie feasts on his corpse until he's discovered.
- After leaving the area, the research facility blows up.
- Later, in Sector 2, Maurice is killed. Samus first learns of a mysterious traitor, who then attacks her. The individual escapes.
- A short while later, we see one of the marines kicking another's corpse into the lava in Sector 3.
- After picking up the trail of Little Birdie, Samus learns the creature is a Ridley clone. She and Anthony fight the monster, and Anthony appears to plunge to his death.

"Hey Samus, why haven't you friended me on Facebook yet?"
At this point, Samus surmises that Adam knew about the traitor in his midst. Communication with him is suddenly down, likely to disrupt the remaining marines' coordination. Samus begins trailing an unknown member of the platoon, who tries to hinder her progress by retracting a bridge and destroying the control terminal. As a side note, this is the first time in the game Samus actually does something of her own intuition without Adam's explicit permission—looks like she's gotten over that post-traumatic stress disorder from losing the baby Metroid and seeing Ridley again.
Shortly afterward, we see the Deleter approach Madeline, followed by the sound of a gunshot. Then there's the whole dramatic scene where Samus learns of Adam's involvement in the Metroid cloning program, and sees Adam sacrifice himself while blowing up the entire Sector Zero. There's a bunch of other stuff that happens relating to Madeline, Mother Brain and an android gone insane, which I'll omit for the sake of focus. Meanwhile, James Pierce is found dead at the spot where the Deleter had confronted MB, while MB remains alive! Suspicious!

Whodunnit: Space Edition
At the end of the game, Anthony is found to have narrowly escaped death during the scuffle with Ridley. Everyone else from the platoon is confirmed dead on the pause menu's character roster except K.G, who Samus writes off as missing. By process of elimination, K.G. must have been the corpse the Deleter disposed of in the Sector 3 lava. With everyone else's actions throughout the story, the only two candidates who had any chance of being the Deleter are Adam himself, and James. Given Adam's back story and the fact that he spends almost the entire game sitting in his command chair and gleefully watching Samus dehydrating without her Varia Suit upgrade, he is unlikely to be the culprit. Why would he go to the lengths of cutting incoming communication with his own radio, anyway?
The most likely scenario is that James was the spy the Federation placed onto Adam's team, who goes about sabotaging things and killing people. His actions at the Biosphere suggest he was the one who corrupted the computer and blew up the lab. As he was tasked with killing any survivors who may have known what the Fed was up to onboard the Bottle Ship, he eventually confronted MB, thinking she was an innocent researcher. Instead, she turned out to be a psychotic android with the personality of the Mother Brain uploaded into her memory, and he died for his mistake.

"My one dying regret... is that I didn't stay alive."
Why this was never explicitly revealed in the game is unknown, but while an odd choice not to give the proper explanation, it made for some interesting conversation topics around the time the game launched.
Having to work things out for yourself is not only fun, but also fits in with the cryptic style of the Metroid series.
So there you have it. Are my deductions sound, or nothing more than insane conspiracy theories? Does it really matter? Any theories of your own to share? What say you, fellow sleuths?