EVE Online/WMG

The Pod Pilots are Cylons.
Specifically, Hybrids. Same neural interface. Same "Goo bath."

The bright star that appeared and disappeared in the sky all over the game world is the EVE Gate.
The EVE gate, specifically, as it collapsed back in the Milky Way ever so many centuries ago, and just became visible to the denizens of New Eden.
 * If New Eden was in another galaxy, this would not be possible for many millions of years after the catastrophe at the very least. If that is in fact the EVE Gate, then we are still in the Milky Way Galaxy.
 * The bright "star" defies the known laws of physics. It is/was a perfect black body, emitting in the entire electromagnetic spectrum, and its light reached every system in new eden at the same time, meaning that the light did not travel at the speed of light; it got there instantly: "The thing is a perfect black body," the professor explained, "the emissions are powerful, unbroken and fall across the spectrum, giving us very little insight into what the object is made from." ... "There is no discernible physical structure in the vicinity of the object," he concluded, "if it was a supernova, the ejecta from the explosion would be visible. Similarly, a large object such as a black hole would be detectable by its accretion disk and by its distinctive polar radiation. This thing has no structure at all. It's like an unbelievably hot singularity, that just popped into existence out of nowhere." ... ""The laws of thermodynamics may not be the only physical laws that are being violated by this object," he conjectured. "If this object is two-hundred light-years away it would take two hundred years to reach us in the Federation, with a variation of several years depending on which system you are in. For its light to appear in every system in known space at the same time simply doesn't make any sense. We've witnessed a physical impossibility!"

The Quafe soft drink company uses recycled radioactive waste to make their drinks.
Seriously, check out Quafe Corp's buy orders some time.
 * They also buy minerals and bog-standard garbage...

The cloning technology to resurrect dead pilots causes them to lose their souls.
The Amarr Holders certainly believe this.
 * In a way, they're right. They aren't resurrecting {you}. They're merely creating a clone that thinks its you.
 * Uh, no, if you read the EVElopedia articles about capsules and cloning, they specifically state that if a pod is so much as even scratched by a stray rock, the capsule will scan your brain (and promptly flash-murder your brain) before transmitting the "transneural data" across space and to the station where your clone is being held. So it's more like reincarnation.

The EVE gate actually led into the past...
... and we are Stable Time Loop living out the past of our own galaxy.
 * Or we could still be in our own galaxy, just not in the past. A single galaxy is a very big place.

The entire universe is an Ironic Hell
The Jovians are demons, and the ruins of ancient societies are actually metaphorical representations of the civilizations that the condemned souls inhabited in life!
 * The Jovians, the game's Sufficiently Advanced Aliens, have a whole orchard of Epileptic Trees. Theories range to them being the a malevolent but brilliant representation of the next state of human evolution, a subconscious manifestation of humanity's darker instincts made flesh, to actually being a manifestation of the game's developers, toying with their creation -- and there is actually canonical evidence to support all three.
 * Then there are the wild theories about EvE's Metagame and developer corruption -- and some of those turned out to be true!
 * It was also suggested through in-game news that the "bright star" was in fact the catastrophe at the EVE gate... at the other end back in our system as seen by the rest of the universe (if that makes sense), obviously it has taken this long to reach us due light taking time to cross the interstellar void. Some NPC nutjobs are setting out for it at conventional/sublight speeds, probably never to be heard of again, except maybe as a Deus Ex Machina to introduce the later, more advanced technology levels? Oh look, a new Tree grew up right there!
 * "T10" or Tech 10 is supposedly Terran technology. The best technology at the disposal of mankind as we know it is "T2", or Tech 2. Assuming the catastrophe didn't wipe out mankind at the source, and what "we" have now is what "they" had then, things on their side could have changed a lot.

Scotty the Docking Manager is God.
He's everywhere, and he seems to hate EVERYONE.
 * Scotty has also been theorized to be at the head of a vast conspiracy that controls the world...I knew the details once upon a time, but they weren't his invention and that was a couple clones ago.

EVE Online is, in fact, a live-action TV show, and not an MMORPG. Players just haven't gotten it yet.
Someone seems to think this, based on where it is on the main page!

Eve Online takes place in the future of The World of Darkness.
Murderous, mysterious groups called "The Seven"? Good people dying but not staying dead? Both franchises are owned by the same company? Ancient and terrible secrets? IT'S SO OBVIOUS!
 * Considering that CCP, the company that created and maintains EVE, merged with White Wolf, maybe there's more going on than we realize...
 * Most would object to describing eggers as "good."

Chribba is the secret leader of CONCORD.
How else does he get away with owning a dreadnought in hisec?
 * Chribba is actually Scotty, and thus God (see above). CONCORD can respect that.
 * Alternately, CONCORD is afraid that if they annoy him, he'll sell off some of his stockpile of Veldspar, thus completely crashing the market for it and screwing up the economy in unforseeable ways.

Admiral Alexander Noir was an Enheduanni sleeper agent.
Sudden change of behavior that causes chaos and the death of the subject? Classic behavior for a sleeper agent. The Enheduanni are planning to weaken the Empires with warfare, then move in themselves.
 * Or... he was one man who went off the deep end. The existence of conspirators does not necessitate every tragedy being the result of a conspiracy.
 * This is answered in the Novelization.

CONCORD ships carry Jovian weapons.
Only the Jovians are capable of producing weapons like those of CONCORD.
 * Also confirmed by the novelization. The Jovians gave a few shiny bits to Concord to.. umm... promote universal piece and harmony? Why not.

The "Concordokken" actually remotely activates a ship's self-destruct mechanism
CONCORD can only activate the remote self-destruct on Pod-Controlled ships, because of the way a pod is tied directly into the control systems. Explaining why they don't just "Concordokken" the various Non-Pod-Controlled pirate ships. Meshing with the previous WMG, the Jovians handed CONCORD the pod API.

The systems just opened up by Apocrypha? The Milky Way, as it is in EVE's time.
Note that initial reports indicate probes placed through the wormhole, though able to report back to them, are unable to identify their locations, sensing it is too far away from them. That, plus the appearance of the bright star in the sky...
 * The Sleepers were created by man...
 * Think about it. The Milky way is the only galaxy that's ever been connected to New Eden by a natural wormhole. The modern wormholes? They're fragments of the Eve Gate wormhole.
 * And early maps of it seem to indicate it's a spiral galaxy.
 * While it's certainly possible that the wormholes could be linking back to the good old Milky Way, there's a lot of galaxies in our universe (a decent number of them spirals). Even our cosmic neighborhood, the "Local Group", has over 50 confirmed members of various shapes and sizes.
 * But another Human-inhabited or formerly Human-inhabited galaxy? There have been no aliens in Eve so far, and Someone had to create the Sleepers.
 * Guess again! Apparently the stars in wormhole space are older then the universe. Welcome to Another Dimension.
 * Except the stars in normal space are also older than the age of the universe. In reality, the star attributes are almost as hilariously senseless as the planet attributes, and little more than filler text.
 * Or wormhole space could be another star cluster in the EVE galaxy. Seriously, one galaxy can have a hundred billion stars in it. New Eden has 5000 stars, and Wormhole space has 2500 stars. They both also have a large preponderance of nebulae which gives outer space its characteristic colors. We've also been aware of the Talocans (who apparently have a connection to Sleepers and left structures in their space) long before we gained access to wormhole space. There's also the distinct possibility that New Eden and Wormhole space are both in the Milky Way, otherwise we'd never have been able to see the "Bright Star" until millions of years in the future.
 * Both Word of God and the backstory proper insist that the cluster just simply isn't in the Milky Way; while it's never really explained how early colonists knew they weren't in Kansas anymore, something like a glaring lack of Sagittarius A* might be a good hint. As for the Bright Star, that was never established as being the Eve Gate.

The 'Dead Storms of the Detorid region are actually small Warp Storms
They seem to occur on a slightly smaller scale than warp storms normally manifest on, enveloping planets by default rather than entire star systems or regions of space, but aside from that, Dead Storms appear to share a great many of the same properties as these larger tears in the fabric of space. S'just that no ships in EVE are equipped to enter the Warp (not that many ships in Warp Storms' home setting are capable of using them to get into the Warp without being torn to bits, either).

Scotty is a Time Lord
And the stations are his TARDIS. In fact there is only one station in Eve, it just has an active chameleon circuit, and is traveling through time to appear to be at multiple places at once. This explains how Scotty is able to be at every single station, because they are all just one station. Stations are obviously bigger on the inside, just look at Jita IV-4 and watch the never ending train of freighters. Furthermore it explains a station's ludicrous resistance to damage, it's a TARDIS defence system.

The Jove are extinct.
Their war with the Enheduanni was mutually destructive. There's nobody left alive in the Jove regions.
 * Disturbingly enough, this one just might be true. Or, at least, mostly true. At minimum, Sansha's Nation is using Jove space as a base of operations for their resurgence.
 * The SOCT contains at least some Jove and is based in Geminate, and several Jovian corporations have active stations in Empire space. It's also possible to gain and lose standings with them. This doesn't entirely disprove this idea, though - Jove space may indeed be lifeless, and these are the only Jovians left.

The design of several Caldari ships was a failed attempt at psychological warfare.
They were intended to be so horrifying that the enemy would be demoralized.
 * The Dominix is the Gallente counter-attack.
 * If you'd like a horrifying thought, the Exequror was—according to The Art of Eve—originally a battleship design. /shudder

Eve Online is part of a plot by CCP to take over Iceland.
The total collapse of the Icelandic banking system has conveniently left CCP as practically the only profitable corporation left in Iceland. They are strong, while the rest of the country is weak. And EVE's massive PVP battles are mere practice for the day when the players will be called upon to act as CCP's army and occupy Iceland.

The Jove control all four Empires.
Coinciding with the arrival of Faction Warfare, three of the four Empires mysteriously changed leadership - Maleatu Shakor replaced Karin Midular as the Republic's leader, and he effectively dissolved the Republic Parliament as well. Jamyl Sarum returned from nowhere with a Terran superweapon to conveniently save the Empire and make herself Empress over the Theology Council's (quiet) objection. Tibus Heth rose from organizing a labor strike to head of the Caldari State almost overnight, while the man everyone expected to take the helm, Otro Gariushi, had a supercarrier dropped on him. Related to this is the power shift in the Gallente Federation, with then-President Souro Foiritan establishing the Black Eagles, a paramilitary secret police, under the command of Senator Mentas Blaque, a notoriously hard-line anti-Amarr anti-Caldari politician. President Foiritan was later replaced in a normal Gallentean election by Jacus Roden. Only the Jove or their rivals the Enheduanni would be capable of such a spectacular coup. This chronicle strongly hints that this is the case.

Faction Warfare is an elaborate plot orchestrated by all four Empires and CONCORD to keep capsuleers busy fighting each other.
Capsuleers are capable of doing a lot of damage to conventional Empire navies. All of them know this. The best way to keep them out of the Empires' hair is to keep them fighting each other. While the initial assaults by the Caldari and Minmatar were certainly cases for war, the war efforts appear to have largely petered out and now focus on a bunch of capsuleers fighting over a group of generally unimportant systems. This is an ideal solution for everybody, as it keeps these ultra-dangerous super-pilots fighting each other instead of causing trouble.

We will eventually rediscover the Milky Way.
But rather than finding a super-advanced civilization, we will find a galaxy in ruins, the result of a war waged with terrifying weapons. Conveniently, the gate system survived untouched. Players will be able to scour debris fields and blasted planets for Terran artifacts, while fighting off the survivors.
 * Who's to say that Wormholes don't lead back to the Milky Way, but they just haven't been charted yet, and thus, can't be claimed?

The Caldari State's Charon freighter design was stolen from the Gallente.
Like there's any other explanation for the Caldari using Gallente naming conventions.