[[WMG: FTL is the future of the Re-imagined Battlestar Galactica Universe]]
Note: This ignores every episode after they found Cylon earth

Unable to reproduce or resurrect the Orthodox Cylons started using genetic engineering to extend their lives. After many human life times they had modified them selves to the point where they were no longer humanoid and could reproduce though [[http://en.wikipedia.org/wiki/Fragmentation_(reproduction) fragmentation]]. After the Mantis rebellion the Slugs retreated into a nebula and isolated themselves for a millenia before re-emerging.

The Orthodox Cylons - in order to create a more reliable army - use human and insect DNA to genetically engineer solders to replace the the centurions. These insectoid solders eventually rebelled and built their own society.

After the Colonials and Rebel Cylons left Earth to find habitable home the colonials and Rebel Cylons split, going their separate ways. The Colonials - using some Cylon technology they gained in the brief time they allied with the rebel Cylons the developed medical nano-machines designed to heal injuries. Eventually every colonial had those nano-machines in their bodies. The nano-machines replaced their blood cells, immune system and the nano-machines "enhanced" their biological parts. During the prodo-Engi phase of their development the colonial society became a class society with the descendants of the followers of Bultar becoming a priest class and effectively the leaders of colonial society and the rest becoming a worker class. This split caused the two classes to evolve in different directions, with the worker class becoming the Engi and the priest class becoming the Zoltan.

The human Rebel Cylons eventually figured out why they couldn't reproduce with each other. After figuring out the problem they were able to solve it medically and began reproducing which is why the human men and woman all look the same in the game.

The Rebel Centurions eventually broke away from the human Rebel Cylons. The Centurions experimented with new technologies eventually taking a form that was nether mechanical nor biological. In this new form they eventually became the Rock Men [[spoiler:except for a small group that separated from the rest of their society.]]

After many millenia and many wars the new races decide to form the Federation to prevent the wars of the past. For 2000 years, the Federation did it's best to keep peace between the races but in time the Federation grew corrupt and began collapsing from the inside out. A group of Rebel human Supremacists took advantage of the of the now weakened faction. They planned on destroying it and in its place, build a human supremacist government that will rule over the other races.

[[WMG: The Federation is TheEmpire]]
What sort of Federation would these guys have been running not to just get routed by terrorists but a full massive scale ''rebellion''. The rebel fleet is unimaginably vast- there's no way they could get that many people on their side without having a really good point. Plus, they keep mentioning the better world they're trying to create. Also, the Zoltan and Engi are allies of the Federation but they don't seem particularly close allies - it doesn't take much (a misunderstanding, merely entering certain sectors) to get them to want to wipe you out of space.
* Contradicted by certain random events, where a Rebel ship will let you go, *if* you don't have any non-human crew onboard.
** In earlier alpha builds (such as the one briefly released to drum up interest for the kickstarter) the Federation ''was'' referred to as the Empire. However, various dialog with the Rebels indicates that their main ideology is space racism, so they still aren't the good guys.
** I prefer to read the Rebels as a military coup (of space racists) against the peaceful Federation government. This A) explains why the rebels have so far managed to kick the Federation's ass and B) makes them come across as something other than an underdog heroic rebel faction.
*** Despite what ''Franchise/StarWars'' (and probably more influentially, the American Revolution) would have you believe, a rebel group fighting to overthrow a vast government is not automatically "Good." The Bolsheviks and the militants that fought over Weimar Germany come to mind. Sadly enough, the world doesn't run on [[TheRevolutionWillNotBeVillified the trope of a noble resistance all the time]] or the trope that you have to have a really good point to get people on your side. Just what *sounds* like a really good point to them. A good comparison is the Gallian Revolutionary Army/Rebels of VideoGame/ValkyriaChronicles and more Communist and Islamist insurgencies than you can shake a stick at.
** When you enter an Engi sector, the game will tell you that times have been tough for these guys since the Rebellion; there are also random events where the Engi will say that your mission gives them hope. And the Engi are so {{Adorkable}}! There is no way the Rebels can be good guys if they're mean to the Engi.
** There's all those evil-looking drone ships the Rebels use... somehow, those soul-less death-bots just do not scream "we're the good guys here!"
** Anyway, it's a fun subversion of the usual "Rebels are always the underdog good guys" trope.
* Not especially relevant to the game, but *every* bloody, vicious dictatorship on Earth has talked constantly about the better world they're trying to create. Learn to sift propaganda.

[[WMG: FTL takes place in the distant future of VideoGame/{{Portal}}]]
* Why else would you be fighting off hordes of mantis-men in the hallways of your disintegrating ship?

[[WMG: You do not play the captain]]
After all, where is the captain character on board the ship? Why can you see and control the whole ship, except when the cameras are down or the door control is down? Why can you fire weapons however you want until power or weapons are shot out on the systems? Simple. There is no defacto captain. In the absence of one as a result of such a poor situation, the ship's AI is forced to take over and help run things. The ship goes down with no crew on it? The AI can easily be turned off in an instant and there's nobody on board to fight it off. You play the AI, not the captain.
* Clearly, the primary purpose of the crew is to act as a fail-safe to stop the AI (that is, ''you'') from going on a maniacal galaxy-wide killing spree. Case in point, you (that is, the ship's AI) can open all the doors and murder everyone in ten seconds. But did you remember that the ship ''must'' have a flesh-and-blood (rock, biomechanical...) pilot at the helm to engage the FTL drive? No crew, no FTL. No FTL, have fun drifting aimlessly in space. MutuallyAssuredDestruction, AIIsACrapshoot style.
** That is a terrifying thought, and I love it. This is now added to my headcanon above.
*** You, being the all-controlling AI, can also control the crew due to neural implants. If you want to be a jerk and send the {{Adorkable}} Engi crewmates to their deaths by Mantis-men or ship-fires, you're welcome to. No one's stopping you. But you won't be able to use their excellent repair skills to your advantage now. It's a strange combination of symbiosis and MutuallyAssuredDestruction.
** This does have some evidence through out the game. Unmanned Drones show it is entirely possible to have a ship run by AI. The Rebel Flagship can have the AI take over the fight if all the crew are killed. You can still control the ship if your crew have been teleported to the other ship. There is also the [[AIIsACrapShoot Trust Worthy Auto-Pilot]] achievement for destroying a ship with the crew still on it.
** More evidence for "You are actually the ship AI" is the fact that you can give orders (open/close doors and airlocks, move power around, aim weapons) while the game is Paused. This can be explained as you being able to move at the [[ComputersAreFast speed of a computer]], that is, near-light-speed.
* Alternatively, the Captain is in another sector giving the crew orders.
* Another alternative, the crew is connected in mild HiveMind where they keep their personalities, but are prone to focusing on other systems/people that they can lose track of their own health/safety.

[[WMG: The Rebel Flagship is the central control node for all the drone ships in the rebel fleet]]
* It would explain why there are so many unmanned ships working for the rebels, how the rebels won the initial battle, and why destroying the Flagship cripples the rebellion.
** Better yet: The Flagship's being a control node also includes it working as a sort of firewall. So the ones that don't simply shut down and stay that way can, in theory, be taken over by the Federation, which would really throw a wrench in the Rebel's strategy of using Auto-Scouts/Surveyors/Assault Ships.

[[WMG: Not only is the Player a AI, but so is the true leader of the rebel fleet]]
* It is said that the data you are carrying is vital to the federation, but who is to say that data can not think? The reason you exist is that your crew managed to replicate the AI from the rebel flagship during the fight. The flagship was originally federation owned and operated, being the first place to use new technology. The AI leading the rebellion was one of these field tests, but its programmer instilled anti-alien feelings common across populated space that result from specialized species taking human jobs (Bob, meet Maxwell the Engi, he is in charge of repairs now.)The AI killed the federation officers onboard and used its drone ships to Zerg Rush and take control of numerous starports, recruiting humans for use in operating better ships than the automatics. In order to defeat a most probably perfect general, the federation needs a duplicate. You.
** [[SelfDeprecation I think there is a fault with my programming.]]

[[WMG: Random-event boarders don't board a ship with Zoltan Shields up; they were there the whole time.]]
->''"You don't know how the intruders managed to get past your Zoltan Energy Shield!"''

* That is to say, they must've snuck onto your ship some time ago, presumably in the cargo hold, but waited until the right moment to make their presences known. (Keep in mind, there is a random event in the Rock Homeworlds where you escort a passenger and they don't show up on your crew list, as they are explicitly stated to be resting in the cargo hold.) Perhaps some part of the Zoltan Ships have an oversight in the form of an area on the ship that does not detect the presence of unidentified life forms, or the intruders stowawayed in a cargo box that blocks anti-intrusion detection systems.
** This is later explained with a Zoltan Shield Bypass ship augmentation. Guess before the expansion pack it existed but wasn't discovered.

[[WMG: The Rebel Flagship's tri-barreled missile launcher is called the "Hades"]]
* Just going along with the Greek theme naming of missile launchers.
** There are people who have managed to view the game program, and found that it is only called "Boss Missile", so no.

[[WMG: The Rebel Flagship has two FTL drives in it. ]]
* This quite neatly explains where its additional reactor power comes from to power all its systems in phase 1, how it can launch drones in phase 2 even when its drone bay is destroyed, how it can flee even when its piloting and engines are destroyed, and how it can regenerate its Zoltan Shield. Power surges occur when the Flagship uses the power of its second FTL drive, and it flees using the second drive when the controls for the first are destroyed. The Flagship also regenerates its Zoltan Shield by jumping "in place". This doesn't really explain why the Flagship has an infinite number of missiles and drone parts, but it's a start.

[[WMG: The three-character string on the Rebels' insignia, "MFK", stands for "'''M'''other'''f'''uc'''k'''ers."]]
* Yes, I know, I act like I'm 13.
** The most widely held belief is that the Rebels are illiterate and their insignia stands for "mankind forever".

[[WMG:The Rebels are the [[VideoGame/{{Ingress}} Resistance]].]]
* The Enlightened, guided by the Shapers, develop interstellar FasterThanLightTravel and use it to explore extraterrestrial civilizations. The Resistance is not fond of this and form an anti-alien Rebel Fleet to assert control over these alien civlizations. As part of their plan to bring humanity and machines together, the Resistance also develops a variety of AI systems, including the ones used for the Auto-series of ships and for the Rebel Flagship.

[[WMG:The entire game takes place in a split-timeline continuity]]
* One thing that is unusual about the game is collecting ships. How exactly does that benefit the Federation? It is clearly stated that if your ship does not stop the Rebel Flagship than the last Federation base is destroyed. The answer is that the ship you pilot on your first playthrough was sent back in time by a last holdout to stop the Rebels. It explains the data you possess, how the ships you collect can be used, and works for both victories and losses. If your ship loses, then the timeline continues unaltered and a ship is sent back in time. If your ship wins, then a ship is sent back in time to close the loop and help other timelines. The Federation "randomly" sends a ship back, which is represented by the player's choice of ship. Also, the ship schematics are either beamed into a computer or the ship itself is delivered to the Federation shipyard that houses whatever device is used to send your ship back in time. This also explains why the general setting is never altered between playthroughs: You've gone back in time to a point where the changes you made to the timeline do not exist. This also overlaps with the "player as an AI" theory, this loony AI (yes, that's me making fun of all of us) is capable of transferring between ships and computers and is sentient unlike Rebel AIs. This allows for the AI to constantly be sent back to try and stop the Rebel Flagship.
** That doesn't explain why the sectors change every playthrough, though.

[[WMG:The Game is a Story or a Simulation]]
* The story being told is of the Human Federation Civilization and it's rebellion centuries before hand. Either the story is being told by another Civilization, a government formed from the Rebels, and/or the remnants of the Federation. The story is either propaganda or a lot of information was lost and no two stories of the Rebellion are matching like TabletopGame/{{Warhammer 40000}}.
** Alternatively, the story is (difficult) simulation given to new crews (or just the ship's officers) to train them for the worse. The Simulations are not supposed to be winnable or are, at least, almost impossible, like in Series/StarTrekTheOriginalSeries as explained by Kirk in Film/StarTrekIITheWrathOfKhan.

[[WMG:Ship's Quarters]]
* This is space. Space takes a long time to traverse. Which means you have to sleep at some point. So where do the crew sleep? [[http://i.gyazo.com/dfede1f36370772af17f5ab6aa6536c4.png I've figured out where their quarters are.]] You may notice that there are only four spaces like this, and the maximum crew size is 8. So how does that work? Bunk beds. That's also why 8 is the regulation maximum crew size, because that's how many beds they have.

[[WMG: The Federation Base during the Last Stand is a heavily fortified bunker, not the fleet or a beacon point.]] In one game of mine, the Rebellion captured the base (or at least its beacon point. I didn't go back and check.). However, I didn't lose as the Flagship wasn't there yet. Presumably the Flagship has some form of orbital bombardment weapon capable of piercing deeper than any old Auto-Assault or Rebellion cruiser, which doesn't come into play against the player ship at any point.

[[WMG: The Rebels are not as numerous as they appear.]]
Yes, they have a massive space fleet that pursues you through the beacons... but the beacons you traverse are only one "branch" off the central federation hub. Federation ships are all off in other "branches" and the rebel branch has been poorly maintained for some reason, so they don't know about the rebels until you come up and point them out. The flagship attack operates under a "cut off the head" mentality; once it's destroyed, the Federation calls in ships from other branches and pushes the rebels back without a fuss.

[[WMG: The Rebel flagship is some sort of rediscovered precursor artifact]]
Think about how amazingly different the flagship behaves from ''every other ship'' you encounter in the game. Think about how much store is set by destroying this single ship. If the rebels had sufficient technology to build another one, why would it be that big a deal? The rebels discovered the ship of a long-lost, super-advanced race and staked their entire rebellion on winning with it.
* Actually, the Rebel Stronghold contains an event where you can fight another Flagship which is under construction. Presumably, this means they have the tech and resources required to build a second one, and the only reason they don't is because you've fought and destroyed it, the Federation gained the upper hand quickly enough to retake the Stronghold sector and halt production of the second Flagship (or better yet, take it for themselves), or (going off the fact that the Rebel Stronghold is randomly generated) the Rebellion simply didn't get time to set up a Stronghold over an entire sector or simply didn't have the resources to do so.
** Okay, that is a mark against the precursor artifact theory, but not necessarily complete disproof. It could be that the second ship is a result of them attempting to reverse-engineer the artifact ship and not completing their work yet. (A good conspiracy theory is, in the end, completely unfalsifiable.)
*** Sadly, as interesting as this theory is, it ain't as simple as that. If you read the event text a bit more carefully, both Flagships were specifically mentioned to be the result of secretly reverse-engineering the prototype Federation Cruiser (well, you were right about the reverse-engineering bit), specifically its artillery systems, which is exactly why it is unlocked by the Second Rebel Flagship event (in which you find it intact after the second Flagship's defeat). So, thusly, no fancy precursor ship, unfortunately, at least in that aspect.

[[WMG: The Federation and Rebellion can be summarized as [[Franchise/MassEffect Paragons and Renegades]], respectively]]
TheFederation believes in cooperation with multiple alien races, and even races that are filled with {{BloodKnight}}s and ConMen (Rockmen, Mantises, Slugs, etc.) [[TokenEvilMinority have individuals who work for the Federation]]. The Rebellion, on the other hand, [[PoliticallyIncorrectVillain are filled with human supremacists]], who often use brute-force tactics and treachery to overwhelm the other races. While [[HumansAreMoreAdvanced they are able to forge more technologically advanced weaponry]], [[HumansAreBastards their treatment of other races catapults them into a morally unjustifiable position]], and [[KeystoneArmy their final assault can still be thrown into disarray if their flagship is destroyed by the player - implying that, once the symbol of human superiority is destroyed with that ship]], [[ThePowerOfTeamwork the united defensive of the Federation would eventually outwit them and beat them back]].

[[WMG: Assuming the Rebellion wins, it will undergo a FullCircleRevolution, and will become TheEmpire]]
Okay, this isn't a WMG so much as it is taking the logical conclusion of how the Rebellion believes in a [[HumansAreBastards Human]] MasterRace, and already institutes heavy-handed "[[PoliceState keep the peace]]" tactics in any sections they take over. Assuming FTL has a sequel exploring this AlternateHistory ([[ForegoneConclusion or not so alternate]], [[NintendoHard considering how easy it will be for the player's ship to get vaporized]]) BadFuture, it will feature [[HereWeGoAgain the player needing to start a new resistance, and begin a campaign to assault the Rebellion's homeworld to dispose of their government]].
* A lot of what's shown in-game implies they already ''are'' TheEmpire, and you're trying to stop them. Several random events say that the Rebels have already one and are basically in charge at this point, hence why the game is so difficult: You're one under-equipped ship, fighting the entirety of TheEmpire by yourself.

[[WMG: Zoltans are mutated Engi]]
They have similar sprites, and are stated to be allies. Perhaps their allegiance is because they used to be the same species, but some mutated (or evolved) into Zoltans.

[[WMG: As a counter to the above theory; The ''Engi'' were created by the ''Zoltans'']]
What's essentially a species of robots couldn't have built themselves out of nothing. Considering how frail and cautious Zoltans are in comparison to other species, it's possible that they created the Engi as upgraded drones who could man ships in unexplored areas for them. Of course, this must have happened very long ago, giving the Engi enough time to outgrow their programming to some extent (though they kept the coding language quirk) and gain territories for themselves. Possibly, that is why the Rebels mistreat them so much despite that they gladly use drones on their own systems: because Engi are technically drones, and/or made by non-humans.

[[WMG: Most Slugs aren't conmen]]
It's just that the ones that aren't have no reason to be talking with you, so they stay out of your way. Since they usually live in nebulae where sensors don't work, it's impossible to see them if they don't want to be seen. The assholes you see in the game are a VocalMinority, [[StopBeingStereotypical loathed by the rest of their species.]]

[[WMG: The Slugs invented the sensor systems used in-game]]
Some Slug scientists studied their natural telepathy, eventually finding a way to get the same effect with technology. They pushed it a little further, and created the sensors in-game.

[[WMG: There are sensor systems that work in nebulae, they just aren't available in-game]]
Something similar happened with the Zoltan Shield Bypass in the Vanilla Edition[[note]]Certain random events would have enemies use it, but the actual augment couldn't be obtained in any way until Advanced Edition[[/note]], so why not?

[[WMG: The majority of Lanius ''are'' friendlier than their reputation would imply]]
Sure, they are often called Metal Demons in-game in areas being attacked by them, and they make ferocious warriors with the whole 'sucking oxygen out of the air and eating metal'-thing. But then we have various quests showing their {{Epic Fail}}s with language (even the best fail to mention that their Translator is [[spoiler:one of their crew]]!) and misunderstanding common customs (waving white flags around), pushing them into {{Adorkable}} territory. And in the "Damaged Lanius Absorbing Jump Beacon" event there's a higher chance that they turn out to be friendly after you give them some scrap/missiles/drones so they won't starve to death or eat the beacon.