Bones/WMG

The Tams descended from Temperance.
Temperance, much like River, shows an intellect that makes everyone else look like an idiot child, she's an expert shot (The Wannabe In The Weeds, she shoots Booth's stalker through her throat with only a quick look, and nobody ever actually said that River was trained in firearms, plus the fact that she stated herself that she just did the math), and genetics don't argue against it. Also, she could see Teddy's ghost, so perhaps it was some low level psychic powers. Plus, it could actually happen, both being Fox shows and all.
 * Adding on, it's not too much of a stretch that if the Tams descended from Brennan, maybe a certain Genki Girl mechanic is the descendant of a certain Genki Girl squintern (and, by extent, a certain plucky psychologist).
 * And maybe Mal is descended from Booth as well, through Parker. Wash through Hodgins and Angela. Book through Caroline. Inara through Arastoo. Zoe through Wendell. Jayne through Fisher. Yes, this troper actually thought about this.

The entire series takes place Twenty Minutes in The Future
C'mon what modern present day Forensics lab has a Holographic facial reconstruction device to SO many touch screen capable (both mounted and handheld) devices for standard equipment??

Hodgins is a spy.
After all, if the US Government wanted someone to spy on the lab, it would be logical to use a conspiracy theorist. Nobody expects conspiracy theorists to be an active part of government conspiracies.

Sweets was Gormogon's real apprentice.
The case for Sweets just fits too well, and the case for Zach is stretched a little too thin. And, canonically, Zach never killed anyone.

Sweets showed up at the right time, threw a small monkey wrench into the Gormogon case, and pegged Zach as the perfect patsy. And now Sweets is Zach's therapist, keeping him from confessing too much. "Sweets: Um, I mean the name of the band is Gormogon. Some people think I'm Gormogon, but I'm not."
 * The secret societies in the government know that the apprentice wasn't really killed. That's why they ran the Jeffersonian labs through that thing in the JFK episode "The Proof in the Pudding" that Sweets identified as a psychological test.
 * Something tells me that
 * A) That a writer for Bones is a Troper, and
 * B) This isn't correct, as it was even mocked in the S4F, "The End in the Beginning".


 * A) this theory was added after the season 4 finale
 * B) You say "mocked," I say "reiterated." They addressed the fact that in the season 3 finale where they discover Zach is Gormogon's apprentice, Sweets was one of the suspects. This is their way of reminding us of that so that, if this theory is correct, it doesn't come out of left field.

Booth's tumor gave him psychic powers, albeit minor ones, a la Jonas Quinn of SG-1
It explains why he was able to escape from the Gravedigger, and how Brennan was able to see Parker in the Cemetery. Booth subconsciously projected the image and voice of Corporal Parker into Brennan's mind.

Booth is not Catholic, or is a severely lapsed Catholic
It seems in character for him to play up his religious background when Bones gets into her more Hollywood Atheist moments to remind her that people don't share her worldview and not to let here worldview interfere with the case.

Note that he seems okay with the idea of ghosts. The Roman Catholic Church isn't.
 * Then again, how many people, Catholic or non-Catholic, actually know the Church's position on the existence of ghosts?
 * I'm an alter server and I believe in ghosts.
 * The views of the church aren't necessarily the views of the individual, but that doesn't make the beliefs of either less Catholic (or whatever other religion)

Lieutenant Parker was the The First.
He's dead, and clearly not a hallucination because he interacted with physical objects in a way Booth couldn't've. Plus, Booth looks a lot like Angel.
 * But the First can't interact with physical objects, either.
 * Hmm, that does make sense, but who's to say he actually did that? Perhaps he gave Booth a power boost for a bit and made it look like he was doing it.

Temperance is a poorly-programmed but incredibly lifelike android sent here by aliens to study humans.
Come on, it would explain so much!

Bones is a Third.
Necessary corollary to the above; given the Season 6 finale.

Booth is actually Angel.
The Shansu eventually came true, he became human and adopted the identity of Seeley Booth.
 * He does have a lot of experience solving mysteries.

Brennan's niece is a Werewolf.
Well, it's true in the book series now, at any rate.

Micah, the security guard who appears in "The Doctor in the Photo", is Brennan's hallucination.

 * Brennan only sees Micah when she is alone.
 * Brennan says she understands what he is saying more easily than she understands anyone else.
 * Despite that and in the many years they've worked together, she has never mentioned him to Booth until that very episode.
 * The biggest issue I see with this plot is that they already did it with Booth.
 * Seeing as the show likes to throw in the occasional Not So Different moment, this might actually be a point for.

Micah the security guard is a ghost
Expanding on the theory above, who else would have all that free time to go to lectures AND be a night guard? Also, no one else seems to know who he is, and Brennan is already talking to one dead person in the episode. Granted, "Bones" doesn't often deal with the supernatural, but this is WMG, it's meant to be fun.
 * Except that, at least sometimes, it does. There are all sorts of Supernatural things (Like the Witch's ghost) that get half-explained by the show, but still make more sense if viewed as Supernatural. Micah definitely seems to count.
 * For all it's worth, Micah means "Who is like God?" and is certainly not the most common name amongst security guards. It fits both as a Meaningful Name if he's something supernatural, and a Cool Name a writer like Brennan would make up, if he is a figment of her imagination.

The Gormogon's final apprentice was black-mailed into working for him
was kidnapped at somepoint during season 3 by the Gormogon. He offered him a choice; a) become his new apprrentice to do his bidding and spy on  or b) be killed and eaten. refused, but the Gormogon then threatened to kill Hodgins if he didn't help him, leaving without much of an option. And to make sure didn't reveal what was happening, the Gormogon kept the threat on Hodgins' life as his black-mail material. Even after is too scared to come forwards, still afraid someone will try and kill him, so he takes the heat.
 * Expansion: Zack has good reason to be afraid. Traditionally, 'Gormogon' was not the only member of the society. We're told in the show that there's only the one pair left, but, we don't actual have any evidence this is the case. They were a whole secret society after all.

There is a long running Myth Arc going on deep in the background of Bones involving the supernatural.
We're supposed to just handwave all the things that we see or are implied away, but in the Last Season it will turn out to be incredibly important.
 * Namely, the barriers between the living and dead have been growing weaker over the series and the weakest point is in the Jeffersonian. By the final season this rift will be reaching a breaking point. This will mean either a) the ghosts will try and repair it with the help of the Squints or b) Zombie Apocalypse.

Hodgins is Batman.
He's insanely rich, so he has the resources to pull it off. Not to mention that he's definetly a little bit crazy, which anyone would have to be to become Batman.
 * Would that make Zack Robin?
 * That would explain why Zack and Hodgins live together.
 * And Zack just seems like sidekick material.
 * Or it could possibly be Sweets. Hodgins one referred to him as a sidekick and they've been on a "secret mission" together.
 * That was the time Angela's dad made Hodgins  as a test of character. Sweets just tagged along.
 * Maybe that was a test of character for Sweets too, except from Hodgins instead of Billy Gibbons. He wanted to see if he'd make a good sidekick.

"Bones" is an alternate DC universe
Inspired by the WMG above. The situation is either a) Squints are the Justice League in this universe, albeit, a more literal one, or b) They are alternate versions of the superheroes. Hodgins, as stated above, is Batman, Zack and Sweets are Robin (the latter replacing the former after the whole Gormogon mess), Brennan is Wonder Woman (she already has the costume), Cam is Catwoman (Again, costume) and Booth is Superman.
 * Wendell could be another Robin.
 * What would that make Angela?
 * Maybe all the Squinters take turns being Robin.
 * Angela would either be Batwoman or Harley Quinn.
 * Or Talia. She and Batman did have a kid together.
 * And if Angela is Talia, that would mean Billy Gibbons is...
 * Billy Gibbons. There is no superhero mightier than him.
 * Also, Daisy would be Harley Quinn.
 * If we go into villains, Howard Epps would be the Joker.
 * That EMT who scared girls to death in season 3 could be Scarecrow.
 * The Gravedigger would probably be Poison Ivy or The Riddler.

The Jeffersonian is part of The SCP Foundation
It's a well funded organization with quirky scientists and we know they also have a large amount of artifacts in storage (what with it being based off the Smithsonian and all). Maybe it's a storage and research facility for them?

Brennan will become pregnant.
Since Emily Deschanel is now expecting her first child, we can presume Brennan may also end up expecting a little Squint, possibly reviving the plot thread from the end of season 4.

Bones became pregnant in the first truly emotional decision she's ever made.
It's implausible that she just forgot to stay on the pill or fish out one of Booth's unused condoms. She wanted to get pregnant so that if something happened to one of them (not hard to imagine), the other would have someone to remember them by.

Brennan is slowly breaking down, leading to her Character Derailment.
Brennan's understanding of idioms and social mores tends to swing wildly, especially as the seasons go on. This is because her own personal problems (let's face it, she's got Asperger's) combined with the stress of her work are taking their toll.
 * Oddly enough, it's making her more humanistic, rather than more Data-like.
 * This is basically canon. She  in "The Doctor in the Photo". That whole episode is about Brennan realising her fear of real relationships and emotional connections is a flaw rather than a strength. This is either Character Development or Character Derailment depending on your perspective.

Hodgins had Goodman fired.
He pulled his influence and had him dismissed after one argument too many.
 * Hodgins usually has a strong Screw the Money, I Have Rules bent, so this would be serious Character Derailment.
 * If Goodman threatened to fire Hodgins (or someone else that Hodgins feels close to, like Zack or Angela), then it's possible Hodgins would have had a few strings pulled behind the scenes to have Goodman replaced.

Because seriously. As Brennan previously said,
 * This needs to be canon, or at least a fanfic.

Micheal S.V. Hodgins grows up to be Agent Mulder
Again, inspired by the WMG above. It's not too hard to imagine paranoid conspiracy theorists run in the Hodgins family. Plus, maybe his Uncle Booth rubbed off on him. Because this is WMG, lets ignore the huge time/name/everything else flaws.
 * Adding on, it's not too much of a stretch to assume, growing up to becoming Agent Scully.

The series will end in a Distant Finale.
At the wedding of the adult Baby Hodgins and, making Bones and Angela sisters in truth, as well as in their hearts.
 * Now that we know it's, this is entirely possible.

Gordon Gordon Wyatt is a Timelord.

 * Ok, Ok... Sorry.
 * They'd never do it, since Stephen Fry is a Timelord and wouldn't want to give people that strong a hint.
 * ...And Gormogon's The Master. Shut up, it makes sense.

There will be a Zombie Apocalypse episode
If only for Rule of Cool / Rule of Funny. The Squint Squad will band together to survive the dead rising in the Jeffersonian, while Lampshading the impossibility of their situation. In a flip, Sweets and Fisher will be the resident badasses for this due to being Genre Savvy geeks. The episode would end with it being All Just a Dream of Booth's.

Brennan will lose the baby
It seems like it would mess up the show a bit. Brennan seems unlikely to have the child then leave it at home the whole time she's at her (very time-consuming) job. They're also not going to show her having an abortion, so it seems likely that during some case or other, she's going to be injured in a non-permanent way that nevertheless costs her the child.
 * Practical for the show, given that writing the baby in in any meaningful capacity would be tricky, and the loss would provide good emotional trauma as an excuse to keep her and booth separate for a bit longer, and continue the long-running UST without awkward break-up episodes.
 * Given that the show is as much about Brennan's evolution as a person as it is about the cases, having a miscarriage this far along, which would just serve to undo all her Character Development, smacks of a Diabolus Ex Machina. More likely, she'll have a close call, which will cause her to stop intellectualizing and truly consider her impending motherhood.

Brennan will have an impaired baby
Brennen assumes that any child she has will be exceptional, but she will end up with an intellectually and/or physically challenged child and have to cope with that.

Booth is NCIS Leroy Jethro Gibbs' nephew
We know that Booth's grampa and Gibbs' dad are the same actor. It does explain why Booth is so Badass and such a good sniper.