By now, I'm sure that many of us Metroid fans are speculating wildly about the finer points of Metroid: Other M. If you've been living under a rock this E3, Metroid: Other M is a new Metroid game by Team Ninja (the Dead-Or-Alive people). The game trailer looks promising, and all the fans are elated.

There have already been speculations about the release date of the game. Some say that 03/25/2010 is the perspective release date, since the HUD read 3 life, 25 missiles, and a big 2010 at the end of the trailer. I am not here to speculate about that.

I'm here to talk about plot. I believe that this game is "yet another reboot" in the growing trend of series reboots. The very presence of Huston and Cpt. Adam Malkovich seem to indicate a pre Metroid 1/Zero Mission setting. Many of the visuals in the plot cut scenes seem to be inspired by the Metroid Fusion Manga. While this manga was never released in America, fan-translated versions are available for the enterprising Metroid researcher.

When I watched the trailer most recently, I noticed that the scenery in the beginning matched the architecture of the Federation Capital. Adam looks like he was lifted right out of the Manga as well.

The biggest no-brainier is that this game will involve the Mother Brain in some fashion. She appears in the trailer. I think her role will be considerable, since Other M anagrams to Mother. Below is my theoretical plot summary, which contains spoilers revealed in the Fusion manga.
[spoilers]
The Mother Brain begins life as an entity friendly to the Chozo. It's purpose is to act as a control system to the dangerous guard-dogs of the Chozo known as Metroid. Samus starts the game at in her late teens/early twenties, acting as liaison to the Federation Military/Police.

Unbeknown to her, the Chozo are preparing a colony ship out to SR-388 from Zebes. This colony vessel is stuffed to the gills with Metroid. The intent is to let the genetically engineered life-sucking super-predators colonize on SR-388 in order to kill the X-Parasite, and make SR-388 'safe'. (Or at least make the galaxy safe from the X that live on SR-388).

Samus goes on some missions for the Federation. A few hours into the game, the Federation receives a distress signal from Zebes stating that it has come under attack from the Space Pirates. Reports show Space Pirates and Metroid making short work of the Chozo. They are on a genocide mission. The Federation decides the best course of action is to blow Zebes up. Eliminate the Pirates before they can gain a foothold, corrupt the advanced Chozo technology, and export the Metroid.

Samus is sent on a last-ditch effort to find survivors of the Chozo, to aid in their evacuation, and neutralize the Metroid threat. She only has a handful of hours to do this, before Zebes and every living soul on it is Atomized in the interest of Galactic security.

It'll be no small task. The Space Pirates are entrenched. The Chozo are dead. The Mother Brain has turned from a peaceful Metroid manager, into a vicious entity with aspirations of Galactic domination.
[/spoilers]

In short. Other M = Mother = Mother Brain. This game is about the origin of the Mother Brain.

[update:]
So.. it looks like this game is actually set between Super and Fusion. That really kills my whole notion of the Metroid canon. But, oh well... the Metroid writers seem to replace the "finer" details whole-cloth when it is convenient. Large portions of my theory still stand... more or less. At least my final statement still stands. This game centers around the Mother Brain. (Were the ones in Metroid and Super Metroid clones? The mystery continues.)