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.
The entire series takes place Twenty Minutes In The FutureC'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.
Booth's tumor gave him psychic powers, albeit minor ones, a la Jonas Quinn of SG1It 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 CatholicIt 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.
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.
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.
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.
Micah the security guard is a ghostExpanding 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.
The Gormogon's final apprentice was black-mailed into working for himZack 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 the Jeffersonian or b) be killed and eaten. Zack refused, but the Gormogon then threatened to kill Hodgins if he didn't help him, leaving Zack without much of an option. And to make sure Zack didn't reveal what was happening, the Gormogon kept the threat on Hodgins' life as his black-mail material. Even after the Gormogon is killed, Zack is too scared to come forwards, still afraid someone will try and kill him, so he takes the heat.
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.
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.
"Bones" is an alternate DC universeInspired 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.
The Jeffersonian is part of The SCP FoundationIt'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.
Hodgins had Goodman fired.He pulled his influence and had him dismissed after one argument too many.
Brennan and Booth's child will grow up to be Kim Possible or Buzz Lightyear from Toy Story or Buzz Lightyear of Star Command.Because seriously. As Brennan previously said, any child she would have would be exceptional.
Micheal S.V. Hodgins grows up to be Agent MulderAgain, 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.
The series will end in a Distant Finale.At the wedding of the adult Baby Hodgins and Baby Brennan-Booth, making Bones and Angela sisters in truth, as well as in their hearts.
Gordon Gordon Wyatt is a Timelord.
There will be a Zombie Apocalypse episodeIf 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 babyIt 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.
Brennan will have an impaired babyBrennen 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' nephewWe 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.
Sully will return and want Bones back.For whatever reason, Sully will come back from Jamaica and want to get back together with Bones. Which will create tension now that she and Booth are together and end with Booth and Sully dukin out. Brought to you by a person who believes Sully is a relationship sue.
In the final Pelant episode, Zack will save the day.Think about it! Pelant is a genius computer hacker, but Zack is genius on an even higher scale. Brennen or Hodgins will eventually go to him for help on dealing with Pelant, and Zack will be able to find the clues the team needs to finally take him down.
We'll be saying good-bye to another Squintern in the final Pelant episode.Remember, during the previous arc against Broadsky, Vincent was killed. And during the Gormogon Arc, Zack was written out of the story. Keeping in tradition, Pelant will probably end up killing one of the Squinterns, finally pushing Booth over the edge and killing the bastard.