King Arthur/WMG

King Arthur was Arthur Kirkland
The entire Arthurian Mythos sprouted from France getting his hands on England's diary and rewriting it to include more chivalry and more sex. "Mordred" might have been a dream England had of the future American Revolution, but got worked into the story for drama.

One or more of the characters is a Time Lord.

 * Merlin. Definitely Merlin. The emponymous Merlin Sickness? He just kept showing up in the wrong order.

Guinevere is sterile.
None of the Arthurian myths feature Arthur and Guinevere having children. This is strange for a royal family, especially one without access to contraception. We know Arthur is fertile; obviously, Guinevere isn't.

This explains why Arthur is so passive about Guinevere and Lancelot's affair. He knows there's no possibility of Guinevere bearing Lancelot's child and affecting the royal inheritance.
 * That's canon in many adaptations. In at least one, Arthur is forced to declare Mordred his heir.
 * Jossed in one-third in Arthur, King of Time and Space, but almost confirmed in another third. In the current-day arc, Guinevere recently found out that she was pregnant. Arthur has already said that it'll be named Mordred (the ultrasound showed it was a boy). In the fairy-tale arc, Guinevere is almost certainly sterile. In the future arc, Guinevere is "putting off having children because of her career".
 * At least three revisions say this. The Mists of Avalon says that a priestess of Avalon cursed Guinevere. At the end of Sword Of The Rightful King, the Sweet Polly Oliver Guinevere is cursed by Morgana le Fay herself -- her "line [will be] blighted, and her cause be slighted." On the other hand, in Susan Cooper's The Dark Is Rising series, Arthur and Guinevere do have a baby, but the kid is spirited off to hundreds of years in the future for his own safety. Finally, in Rosalind Miles' Guinevere series, she does have a child - a little boy named Amir. He dies at the age of seven in battle with the Saxons, cursed by Morgan.
 * In 'The Mists of Avalon,' it's Morgause who curses Guinevere because she figures out that Mordred (her foster son) is Arthur's biological son and fancies herself as rightful High Queen of Britain. Or something like that.
 * That said, how would Arthur know for certain that she was sterile? If she's young and in good health, then that's quite a claim to make.
 * Because they both can count, and they would have spent the first years of their marriage working double time to produce an heir.
 * By the time of the whole Lancelot mess, she wasn't particularly young - some sources have her old enough to be Lancelot's mother. Going that long without a pregnancy would have given him some idea.
 * In the original Alliterative Morte D'arthure, she DID manage to have a kid, with Mordred no less. Squick much?
 * Not so. Lancelot is a relatively new character invented by the French nearly four hundred years after the original legends started. In some of the earliest variations, Guinevere (in the oldest called Ginevra, in newer ones called Jennyfyr or Gwenhyvar) had two children by Arthur, one boy and one girl. The names of the children vary.
 * Lancelot isn't that new. Check University of Rochester's Camelot Project for more information - they've got some good stuff up there. Although Malory's Lancelot is probably what most readers are familiar with.
 * Lancelot may have existed in oral tradition earlier, but the first written account of him is from the middle of the twelfth century in the work of Chretien de Troyes.

Guinevere isn't sterile; it's just that King Arthur is female.
As you know, Saber was once King Arthur. Two girls couldn't have a baby even if they tried.
 * Which also explains why Guinevere had an affair with Lancelot. Poor Guinevere must have expected her wedding night to be awesome, and then she realized 'Arthur' wasn't a...suitable person.
 * Yeah, and Mordred's been conceived in lesbian incest. No wonder his her head is messed up. Imagine how you would feel if you discovered that your dad is your mom's little sister!
 * That would put a damper on this theory, but some versions cast Mordred as the son of King Lot and Morgause-that is, he isn't Arthur's son, just his nephew. Perhaps this version is true, which would make Arthur secretly being female plausible again.
 * In Malory, Arthur gat a son, Borre, never mind the whole Mordred thing. and as said above, he sometimes sires children with Guinevere.

King Arthur is Mordred's birth mother
Hey, who would dare call "him" on the pregnancy? Guinevere is busy, and Arthur is the King!

We don't know who the father is. Given what kind of person Mordred turns out being, we can't rule out incubi.

Or maybe there is no father -- the person named as Mordred's mom in the legends tends to be either Morgan le Fay or Morgause, and both of them practiced magic. Of course, this means that either magic has to create a Y chromosome or the gender-flip is also hereditary.

In addition of King Arthur being female, Guinevere is male too, and he crossdresses as a princess, and he is a convincing Wholesome Crossdresser.
All this is a conspiracy. Well, in this case, they can have children, but King Arthur will be the one who can be pregnant.
 * But King Arthur can't as this will hinder her much more.(She crossdresses as a man to rule the country, so if her gender is exposed, you can imagine the result.)

And with the WMG above, Lancelot is a gay.
Boy x Boy love between Guinevere and Lancelot can be interesting.

King Arthur already returned in England's time of greatest need.
World War II seems to be the most likely time, and Churchill the most likely candidate for Arthurship.
 * Don't forget Sir Arthur Wellesley, the first Duke of Wellington.
 * There's also the red-haired Prince Harry, which does not bode well for the future.
 * Hello? How about Queen Elizabeth I?
 * This can only mean one thing...
 * Sonic is the reincarnation of Winston Churchill?

The real King Arthur is Sealed Evil in a Can
The stories that we've heard are corruptions of the original tales. Arthur was a cruel and murderous warlord who was sealed away on Avalon by Merlin so he couldn't do further damage. But the spell wasn't perfect, and Arthur will return in England's time of need to finish it off.
 * But Merlin will also return to battle the daemon king Arthur. There will be MUCH asskicking!
 * It's worse. King Arthur is an Old One. "IÄ! IÄ! ARTHUR FHTAGN!"

Morganna le Fay loved Arthur
Think about it: she's supposedly Arthur's greatest enemy, hating him because he is the product of Uther Pendragon's rape of their mother. But what does she do to him that's so awful?

Well, she exposes that his wife is having an affair with someone who is supposedly his friend. Then she herself sleeps with him, finally giving him the son and heir he had longed for for years. Then, when he lies dying after killing their son, what does she do? She takes him to Avalon to heal and someday return.

King Arthur will come back
Britain's hour of greatest need will come during a third world war fought between a revamped British Empire and the United States in the 2050s. Arthur will return and lead the British in an invasion of America. However, this will also count as America's hour of greatest need and Captain America will return to lead the United States. The unstoppable Excalibur will strike Cap's unbreakable shield, and existence will explode.
 * And it will be AWESOME.

Mordred managed to have kids before that last battle
It was decided not to let one of them take succession when that last battle happened. But the line survived in secret until the legend faded into, well, legend. Every MacArthur, McCarthy, and McCartney out there is a testament to this, and many of them even carry a little of King Arthur's blood... as well as a little of Mordred's. (It can't be helped.)

All of Arthurian Legend exists in a Multiverse
This explains the various interpretations and conflicting facts, as well as the retellings. All of the retellings of the mythos, from The Mists of Avalon through the Merlin television series are true, just in alternate universes.

Excalibur is a reforged Caliburn
See, the Lady of the Lake named it EXCaliburn, which became Excalibur due to language drift. EX meaning Extra, as in extra powerful, of course. I guess saying it was formerly Caliburn works too...

Merlin is from the future
This explains why he knew what was going on in the future. For the dragons, he just used seismic machines to find out they were there.

Merlin is John the Beloved.
Okay, think about it for a minute. Jesus tells Peter not to worry about it if John stays on earth until He comes back, and tradition holds that that means that John's immortal. John had a vision of the future in Revelations, and was one of Christ's twelve Apostles, with Christ's authority and power. Why would a pagan wizard be an advisor to a Catholic king? And how would an immortal miracle-worker with knowledge of the rest of history who didn't want to be found out explain himself? "I'm a Wizard! These miracles are magic! Oh, and hey, Arthur, we should make England a better place, huh?" Oh, and he told Arthur that the two of them would be coming back to England one day, after their "deaths". Which sounds a lot like the resurrection an Apostle would be preaching.

John the Revelator was totally Merlin the Wizard.