So, here goes:
The Beyonder, in all his omnipotent glory, had grown bored of the wiles of uniquely powered individuals known collectively as "superheroes." Instead, he turned his attention to the race of Humans as a whole, looking into both future and past to witness Mankind's accomplishments. He noticed, with eccentric glee, the many trials and tribulations the species suffered as time progressed, against themselves, and against foreign species.
His power, reaching beyond this universe, was able to peer onto other Human civilizations, in other realities. They suffered many of the same maladies wich plagued the Humans of the universe in which he currently resided. Called to act by what he had seen, his influence spread outwards, encompassing trillions of beings from a smattering of dimensions.
Collectively, he brought them together into a super-galaxy, sealed off from the rest of existance. A galaxy in which a nearly endless amount of raw resources on which these beings could draw upon resided. The multiple Human civilizations he placed on one side, the myriad of Xeno races on the other. He said to each race in turn, appearing before every individual member of the collective species, that they must fight for their survival. One Coalition must win out, no matter how long it takes, for to the Beyonder, time is nothing but a flow of ethereal energy which could be reversed, sped up, or otherwise manipulated as easily as a Terran turns on the focet.
And so, the die cast, each Coalition takes a tentative step forward, much to the Beyonder's satisfaction.
Basically, it's All Humans vs. All aliens. Here are the collective Fictional empires that are warring:
The Imperium of Man (Current)
The Galactic Republic (Star Wars' Clone Wars)
The Federation (Star Trek)
UNSC (Halo) (All Human Forces, even the Insurrectionists) (At the Height of their power, Spartans Included)
Weyland-Yutani Corp (Basically all of the Alien-In-Universe Human civilizations)
The Galactic Empire (I know, two Star Wars armadas...this also includes The Rebellion)
Terran Federation (Starship Troopers)
MechWarriors (These Guys)
Tau Empire (Warhammer)
The Eldar (And Dark Eldar) (Warhammer)
The Covenant (Halo)
The Flood (Halo)
CIS (Star Wars)
Bugs (Starship Troopers)
Martians (The War of The Worlds)
The Goal for each Coalition is to exterminate the other. None may survive.
The Beyonder has resurrected the Emperor of Mankind, to better the morale of the Human Warhammer faction. He has Done Likewise With The Jedi to help the Republic's Morale. The Same With Palpatine and Vader. He has Also Given the UNSC all of their Spartans back (complete with Avery Johnson!).
The Human Coalition will work heavily on spreading out their forces, helping to improve weaknessess in their fellow human armies (Example: The Galactic Republic gives the Imperium of Man some pointers on tactics, while the IOM gives the Galactic Republic increased firepower).
The Xeno Coalition will likewise work on their weak points together.
There is no Warp in this setting. Human Phykers are much more versatile...but oh so limited.
The Beyonder has not only transplanted all of the races armies, but their planets and citizens as well. This Galaxy contains four Earths, as well as all the other planets the humans have conqured, and all on one side of the Galaxy. Likewise with the Aliens.
The Flood have consumed biomass equivalent to the forest moon of Endor, and have given birth to a Gravemind. It is this Gravemind that keeps the Flood on the Xenos' side. If this Gravemind is destroyed, the Flood would become feral, and attack both sides of the war. Keep in mind that they can create another Gravemind.
The Tyranids' numbers are impressive, but not overwhelming. About the average day-to-day population found in the 40K universe.
The Humans must fight Aliens, and vice-versa. A Civil War will result in the extermination of the Coalition responsible. This does not extend to the Flood (or possibly Tyranids) who would, naturally, go rampant if they lost the hivemind motivaiton.
The Beyonder has stated he favors Ground Combat, and so that will be the majority of combat taking place. However, since this war will likely last thousands of years, a great many space battles will probably ensue.
Well, there ya go! As I said, I'm not the most well-read person in these fictions, and some tips would help. Also, if you would like to see a human and/or Alien faction added to the lists, I'd be happy to oblige! Also, a note I may have forgotten to point out in the "Notes" section that would place the battle on a more even footing, if you should find one, please bring it to my attention.
EDIT: The Two factions from the Starship Troopers universe have been added.
EDIT2: MechWarriors have been added.
EDIT3: The Orks (Warhammer) have been added.
EDIT4: Martians (War of the Worlds) have been added.
EDIT5: The Replicators (Stargate) have been added to the Xeno Coalition.
EDIT6: The cool pictures have been added.