His Dark Materials/WMG

Dust is a cosmic computer.
More or less. Dust is a cosmic computer that came about from emergence, and its "programming" determines the physics of any particular universe. It's also "in" "the bulk" (M-Theory).

The Subtle Knife is based on Death's Scythe.
Specifically, the Death of Discworld's scythe, which is sharp enough to sever the connection between a person and their corpse after death, sharp enough to glow from the thaums being split on its edge, and sharp enough to cut through the 4th wall, slicing into the very words on the pages. Somebody tried sharpening a knife made of special alloys over and over, until it was sharp enough to cut the boundary between worlds.
 * They sharpened it with spider silk. And sunlight.

The Abyss isn't just a void.
Or, if it is, it wasn't always.

One possibility: It's a universe that was entirely consumed by the Specters.

The Abyss is the Abyss from Mage: the Awakening.
The Angels are the humans who invaded the Supernal and became the Exarchs and Oracles; in doing so, they lost their bodies. The rebel Angels are the Oracles; the Authority is run by the Exarchs. Lord Asriel is a member of the Silver Ladder, invading heaven to set up an anthrocentric cosmos.

The people who are left in the wrong universe when the Oracles close all the gates that pass through the Abyss don't all die; just their flesh dies. They Ascend and become the rulers of the reality that they're stuck in.

Narnia and our world (the Earth the "Friends of Narnia" inhabit) are also part of the Multiverse.
Dust is also the key to traveling between worlds in Narnia's multiverse, as discovered by Andrew Ketterly in The Magician's Nephew.
 * Making Aslan...an agent of the Authority? Or Tash? Or both?
 * But in HDM verse it's just as impossible to tell the true reason for existence as in the Real Life - the closest implication is that the Dust is God, or God's remains. Aslan ofcourse could be a limited creator with some delusions of grandeur over his role in the grand scheme of things...
 * Aslan is the Daemon of all of the Dust hive mind entity combined, obviously. Making him not a true creator, but a reflection of Dust as a whole.
 * Isn't it obvious? Aslan is Metatron. Why do you think Narnia's stuck at medieval tech level? In Narnia individual thought and initiative are discouraged in favor of trust in Aslan and doing exactly what he says. While the people opposing Aslan might be morally questionable, they all share one common characteristic: they don't want to live in a world where Aslan makes the rules. And at the end, Aslan leads everyone to a place which those who are on his side believe is Heaven and everyone else thinks is their doom. That is, of course, the world of the dead, where everyone remains until Will and Lyra arrive to lead them out.
 * The Authority was a liar and poser; Aslan is the true Creator. Which does give him genuine Authority over the universe he created! Tash could be an agent of The Authority, though...
 * Why would creating something give you authority over it? Sentient beings, no matter who they're created by, have every right to self-determination.
 * But the afterlife in Narnia is a paradise, and the afterlife in His Dark Materials is a shithole and it was stated that ALL souls from all the worlds go there good or evil.
 * But it's also stated that the devout delude themselves into believing it's paradise anyway. So those dwarves in The Last Battle were the only ones who saw the truth!

"Baby" Dæmons are formed through Improbable Species Compatibility.
The fact that Dæmons are incarnate spirits rather than normal animals makes this theory a little easier to take. In Lyra's world, as two humans have sex and concieve a child, so their Dæmon counterparts concieve that child's Dæmon. Said Dæmon may even be born from a Whale Egg or something as the child is born. There is a scene late in the first novel and a small scene in the second novel that comes ascloseasthis to stating this outright. (Personally, I am hoping this will be Jossed in The Book Of Dust.)
 * Then do we really want to know what's up with that one servant guy in the first book who's Dæmon is male?
 * He's obviously gay. Or at least, transexual.
 * Word of God, IIRC, is that having a same-gendered Dæmon says something about one's sexuality, but he's not sure what. My speculation is that it might be a sexual orientation that we Dæmonless people don't have: maybe a man with a male Dæmon is only attracted to women with female Dæmons. Or to either gender, as long as they have a same-gender Dæmon. Or something.
 * Eh, my theory is that they are attracted to their sex, thus making a childless (personless?) Daemon. Or that's what I immediatly thought when I saw this WMG
 * What about rape? Does the rapist's dæmon also rape that of the victim? If not, is it therefore impossible to conceive a child through rape in Lyra's world?
 * In order: Sure. Why not? If that were they case, the result could be a child that lacks a conscience and grows up to be a horrible monster because it's lacking something that children born of a loving relationship normally have, for mystical reasons.

There is a Scientific Explanation for Dæmons.
We know that they have some relationship to Dust. We know that Dust is especially attracted to humans and their activities. Dust in turn has some form of sentience and awareness. So Dæmons are colonies of Dust that have, over the eons, formed a symbiotic relationship with humans. One so strong that, while a Dæmon is not literally his counterpart's soul, he might as well be. The colonies of Dust also gained human-like intelligence thanks to this relationship. This helps explain the Shapeshifter Baggage issue, the eating issue, the Not-Quite-Furry Confusion-But-Similar Dæmons vs. domestic animals and pets issue, and (perhaps most importantly, for our sanity) the baby Dæmon issue: the latter simply form out of the Dust attracted by the newborn human.
 * Isn't this Jossed by what we see of Mary and Will's Daemon's? Will's is literally ripped out of his body and Mary can see hers despite never going to Lyra's world - although Daemon's bodies could reasonably be made of Dust - that's what they turn into when their human dies.
 * Not sure how it's Jossed. The book never says that Dust isn't present in our World, and the colonies of Dust just never coalesced into physical forms in our World. Doesn't Lyra say something after meeting Will that he must have a Dæmon that she can't see?
 * Actually, Dust is clearly present in our world. Lyra finds it on trepanned skulls in a museaum, and Mary's team detected it on carved wood.

None of the divination tricks really work.
Every possible outcome of every chance event exists in some Universe. When Mary Malone casts the I Ching, most versions of her get useless results, but the story only follows the version who gets an answer that makes sense. Ditto for the Navajo ring which supposedly and the alethiometers themselves. When the story reaches a satisfactory conclusion, this doesn't matter anymore, so we start following a version of Lyra who. Naturally, she believes that.
 * That doesn't really work, considering that we never actually see any alternate universe counterparts for anyone. In the entire multiverse, there is only one Lyra Belacqua and one Mary Malone. The reason they were able to work was because the Dust was specifically guiding them to act out their roles, and such divinatory methods were the only way to communicate to them. That ring worked differently, because John Parry cast some sort of spell to bring Lee Scoresby to himself.
 * There is at least one reference to a person in Lyra's universe that also existed in ours: John Calvin, who in Lyra's world became Pope.

If what the books say about the multiverse and imagination is taken into account, then EVERY SINGLE fictional universe actually exists!
Think about it, the whole "imagination and dreaming is a way to make contact with alternate realities" can only mean that.
 * The idea is both awsome and sucky at the same time. Awsome, all our wildest imaginations exist in some form or another as real universes. Sucks, we'll never be able to have contact with them. This theory is looked at with more consequence in the Inkheart trilogy.
 * There's nothing "sucky" about that. That's what we have imaginaaaaaaaaaaation for!
 * It Gets Better : If it contains every single fictional universe, HDM's multiverse contains South Park. Therefore, it contains Imaginationland. Since Imaginationland is all fictional universes put together, it contains HDM's multiverse. Therefore, we have a recursive multiverse.
 * It also means that there is a universe in which the heros fail, and The Kingdom of Heaven defeats Asrial.

There are two different versions of His Dark Materials out there.
There's the one we all read, of course. There is also one that contains a totally unambiguous scene in which two under-ten-year-olds walk up to the Judo-Christian God and shiv Him in the back or something. This would explain quite a bit of the books' Hatedom...
 * Like this theory. Want to subscribe to your newsletter. Ect.
 * Well, now I want to know where I can find the other version. It sounds far more intriguing.
 * There is also, presumably; a third version in which Pullman goes out of his way to specify that the entity that dies isn't really the Judeo-Christian god and that he is really just attacking authoritarianism. This is the version the people defending the book from its Hatedom often use.
 * He's pretty explicit about this in the supplementary material, but he did shoot himself in the foot not putting it in the book.
 * Links or it didn't happen.

Lord Asriel is Jesus.
No, really! From his perspective, the whole plot of the first book is, "Suffer the little children to come unto Me." Right? And then, in the third book, we find out that Metatron is the ascended version of Enoch, whose desire for the solidity of human flesh is driving him psycho. Given his sleazy libido, Metatron is basically Sin with wings, and Stretching this really far, you could say that the reason the Church in the trilogy isn't a warm and fuzzy organization is because the books describe a timeline in which Christianity never diverged from the Old Testament fire-and-brimstone business, and it had to take a Heroic Sacrifice to set things right. . ..
 * You. Are. A. Genius.
 * Seconded.
 * You know what that means? Marisa Coulter is Mary Magdalene!
 * Woah. Whoah. WOAH. Call Pullman immediately, he must comment! Once again, genius emerges from WMG.
 * Metatron runs the Church which condemns lust so his "sin" isn't lust but hypocrisy and self-denial.
 * Intriguing, but isn't "Asriel" supposed to be the reference of a fallen angel/the angel of death/Satan himself? HDM is pretty much A Child's Guide to Gnosticism 101 already, so the Authority is supposed to be an malevolent version of the Old Testament God, but to make Asriel be Jesus AND a fallen angel seems a bit much.
 * Hmm...Azriel is the Angel of Death, no? The one who killed the Egyptian firstborn and so on. There may be dozens of versions of the same figure, though.
 * In any case, it does make quite a bit of sense in the Gnostic context where the Old Testament God was seen as evil, but Jesus seen as the good Bringer of Light (remember the Latin word for that?).
 * Pullman has promised to deal with the Jesus-issue in his future book set in Lyra's world. Maybe it'll illuminate the matters a bit.
 * Also, the book ain't a child's guide to anything. (Just had to be said.)
 * Pullman seems to believe that Jesus Was Way Cool (see The Good Man Jesus, the Scoundrel Christ) so this is possible.

Lord Asriel Has the Power to Summon Things, But Only Once
In book two, Ruta Skadi speaks admiringly of Lord Asriel and all he's accompliced. She thinks that he bends time to his will, and says that he's able to bring, or summon what he needs from all over the world. As a matter of fact, most of Book One is the effect of him "summoning" Lyra to bring Roger to him - a child whom he needs to split open the sky. Lyra can't explain exactly what she's supposed to do or give to her father, she just knows she has to see him and help him. After Book One, she appears to be more or less indifferent to him, even though in Book Three he's expounding all his resources to retrieve her. Why doesn't he summon her again? Because the summoning only works once. After that one time, he has to work on keeping what he has summoned by him. He unwittingly spent the one chance to call her to him (and got Distracted by the Coulter, and now has to try and make everyone else bring her to him.

Daemons are a metaphor for the inner self
Think about it: Children have not yet settled on their future personalities so their daemons can change form, people touching someone else's daemon is a taboo, since it implies that their minds are being tampered with and daemons fight and play with each other due to conversations causing people to get to know another person's inner self. Children separated from their daemon also lose their personalities, and die quickly (lack of activity in the brain). It is implied that the people of Will's world still have daemons, and possibly that every conscious being has one, again relating to the idea that they represent someone's true personality.
 * ... Wasn't it obvious?
 * That was a joke. I hope...

Daemons don't die when their human does.
They go to the world of Alera where they attune their selves to nature or new people, transforming into elemental Furies.
 * ORLY

Xaphania is still loyal to Authority and Metatron
Upset at her side's loss she arrived to the children in order to try and force a happy end into a bittersweet one, mostly by shutting down completely viable ideas.
 * This actually seems viable. She's given very little character development, but we're supposed to trust her as dearly as we'd trust anyone. Hmm....
 * So, given that she was in Asriel's side, this would make her The Mole? Sounds interesting...
 * So she might have been lying? "We calculated the loss of Dust through the hole into the Abyss, and it's exactly enough to let us keep that one one escape hatch you carved and nothing else. And you can't survive near as long as Parry in a world that isn't your own, just to remind you that it's all unnatural, going to be lethal if you try, *boogaboo*. So go home, right now, we'll, uh, have angels seal up all the other portals for you so you don't have an excuse to hang around Ci'gazze. Unless you want to make these people eternally damned. No? Thought so. ([aside]Heh, a guilt trip always works.[/aside])"
 * She was somewhat maverick in her intentions. She really was in favor of Dust being preserved, and therefore fewer windows, but her remaining loyalty to the Authority and Metatron gave her an urge to avenge them on Lyra and Will.

Intercision will be perfected accidentally via an overdose of electricity and become known as Delightfulization.
...Successfully depriving a person of their individuality without killing them but turning them into a soulless zombie obedient to all authority... designed chiefly for use on kids.

There is a reasonably practical alternative to the Subtle Knife that takes slightly less than "a lifetime" to get the hang of.
Sentimental reasons aside, the way this possibility was Jossed and the resulting Downer Ending added nothing to the book except either a very Broken Aesop... or a Sequel Hook.
 * Please explain

Balthamos and Baruch were the only pairing to have a happy ending
Think about it. Angels are made of Dust, right? And Dust tends to condensate, otherwwise there would be no angels, right? And
 * That does seem likely, though then pretty much everyone who died had a happy ending and not just those two angels.

Baruch is named after Baruch Spinoza
The guy who regularly critizised the Church and had a concept of God similar to Pullman's Dust? Sounds like someone Pullman would give a Shout-Out to.

Willing intercision subjects are less severely harmed by the severing than unwilling ones.
Willing subjects who have been severed from their daemons are able to live fairly normal lives, be it without any imagination or ability to question the world around them, while those who have been forced through the process tend to be virtually demolished by the procedure.
 * That would seem to explain why adults in the service of The Church are so high-functioning after intercision. The nurses at Bolvangar and Mrs. Colter's soldiers can do their jobs, where as Tony Costa was in a state of psychosis.

The Intention Craft is based on Psychoframe/Psycommu technology Asriel picked up from the universe of Mobile Suit Gundam
Asriel had many highly skilled engineers from many worlds at his disposal didn't he? Who's to say some former Mobile Suit and Mobile Armor technicians from the Universal Century universe didn't rework newtype mobile weapon technology to take advantage of the physical daemons present in Asriel's homeworld.

Will and Lyra will meet again

 * Guys can't become witches in this world, otherwise the males of Witch-Human relations would go through the same training as witches. It could (But I highly doubt it) mean that Lyra gets this power, but less likely Will...will. She'll live long after he dies and she will know it.
 * Other worlds than Lyra's have male witches, and Serafina says that Will is categorically a witch in the same way as Lyra. Serafina herself says she doesn't know exactly how it'll work, but she's willing to roll with it.
 * I agree. There may be other ways to travel between worlds, especially if we imagine that every fictional work has their own universe (or multiverse) -- and there are definitely plenty of fictional works that contain travel between worlds. Even the Narnia series could be compatible with His Dark Materials. I would be interested in reading crossover fanfic between the two series.
 * Like Planeswalking? An MTG/HDM crossover fic would be awesome beyond belief.
 * I think Philip Pullman might die if this happened, but seconded.
 * Die nothing, he'd explode in a matter/antimatter reaction. Also, given Aslan's genuine messianic and divine reality-warping traits- traits far beyond what we see from The Authority- the question would be raised as to why The True Creator behind Aslan never did anything about those angelic imitators wandering the multiverse.
 * Alternate Theory: The angels can travel through worlds, and Will and Lyra have met several angels by now. Surely one of them might be willing to ferry them to each other's worlds on occasion? I mean, these two basically saved the world.

Mrs. Coulter is Ann Coulter.

 * She's called Marisa by once-lovers Dinesh D'Souza and Andrew Stein Lord Boreal and Lord Asriel several times throughout the series, and towards the end is painted far more sympathetically than Ann Coulter could ever hope to be.
 * This would explain why--after seeing Nicole Kidman play Mrs. Coulter--Philip Pullman said, "You sometimes are wrong about your characters. She's blonde. She has to be."
 * This troper's personal WMG: Philip Pullman made that up, Mrs. Coulter is in fact always intended to be dark-haired, but the simple fact is that when you get Nicole Kidman in your movie you don't complain.

His Dark Materials is bad Fanfic of The Bible from an Alternate Universe

 * (Bear with me here. Also, massive spoilers ahead, and if you're a fan you might want to take this with a grain of salt, I do think these books are very well-written. Sorry, felt that was necessary, putting my hat back on now.)
 * A teenaged girl reading a novel named The Bible posts on the web forums of a fansite about how she is sooo angry that her favorite character Eve got such a raw deal with the whole apple thing and begins posting chapters of her story about Lyra who is Eve reincarnated who is the daughter of the two coolest smartest people in the world ('even though they're evil') and makes friends with everyone she meets, including witches, a cowboy balloonist, a talking polar bear, gypsies, and 'a cute boy named Will with a cool knife that can cut through anything :)'. Lyra goes on a quest to kill the novel's author, God, through the magic of interdimensional planet hopping and after a few snarky comments and bizarre encouragements from various forum posters and moderators, she adds these people to her story as well. In particular a rather rudely-authoritarian moderator who bans her from the forums posting under the name of Metatron suddenly usurps the role of Big Bad, but somewhere in her following rants this story point is forgotten. The next chapters are posted on another website entirely, and take on a very dark and hostile tone setting up everyone on the first website's staff as the most horrendous baby-eaters, even going forth as to portray characters previously seen as villainous as somewhat sympathetic to Lyra's cause, and eventually Lyra succeeds at her goal of slaying the author after portraying him as the most insultingly senile old man who is killed by a slight breeze. However, she 'did it by accident and she kind of felt sorry for him too'. After that point, the fic somewhat loses what cohesion it had had up to that point, ending on a sad note as Lyra and Will, due to something about everyone having to stay in their home universes which isn't very well explained, have to leave each other forever even though they've both suddenly discovered that the other one is their one true love. So sad. If there was any other hooks the author intended to continue the story with to resolve this problem, she apparantly got bored and abandoned the project, otherwise we'd have to assume that the entire point of this exercise would be to bash the author of the original book for the actions of a fan organization who he's clearly not pulling the strings of at all.

Angels are actually Time Lords
Their 'imagination' way of traveling that seems insufficient to Lyra and Will actually works better for the angels. Because they're Time Lords.

Witches are renegade Time Lords
That's why they live so long; they can regenerate. You can 'become' a witch by loosening the link between yourself and your daemon, i.e. becoming a free spirit. The real reason that Lyra and Will aren't full witches is because they weren't Time Lords in the first place. Witches' cloudpine branches are their TARDISes.

His Dark Materials takes place in Magic: The Gathering's Multiverse.
The events of His Dark Materials take place during the Time Spiral block, where vast imbalances of power due to the many near-godlike Planeswalkers caused rifts in the Multiverse that threatened to destabilize all of reality. The consequences for the realms affected were varied: in the case of the collection of universes where His Dark Materials took place, they suffered from the slow drain of Mana (or "Dust"), resulting in the withering of life and sentience. Contributing to this problem was the Subtle Knife, a device that allows non-Planeswalkers to travel between worlds via creating rifts. The Guild of Cittagaze used this to build up their wealth and power, but the Specters it released were their downfall. (These Specters may or may not be related to the Specters of other universes, such as Hypnotic Specter and others.)

The Authority was a very powerful Planeswalker, possibly a protege of Serra's, who went insane and attempted to become like Serra, building a facsimile of Serra's Realm (The Clouded Mountain), creating his own army of angels-slash-Elementals, and attempting to subjugate worlds to his "benevolent" rule. At some point, he went insane and was overthrown by his own creation, Metatron-- who was probably a very powerful mage given the privilege of becoming one of the Authority's angels. The Authority's defeat and subsequent sealing turned him into a raving vegetable, allowing Metatron to go about consolidating the Kingdom of Heaven's power by inspiring Corrupt Churches everywhere to work in subtle ways towards his goal of subjugating The Multiverse to his will while exploiting the rifts to gather a multiversal army. Asriel, seeing evidence of a conspiracy on his world, immediately planned to create La Résistance, and hit upon using the energy of a human being's soul to create a rift where the fabric of reality was weakest: the Aurora Borealis. Once that was done, he began gathering forces from every corner of the Multiverse (explaining the variety of creatures and machines in his army).

Lyra and Will were caught in the middle of this great multiversal war, although they did not realize what exactly was at stake until the very end, where the concept of the rifts was explained to them. As the Planeswalkers gave up their sparks in the Mending, Will and Lyra gave up the ability to be together and travel the worlds in exchange for removing the capability to create new rifts (and thus, making the Multiverse safe again) by destroying the Subtle Knife. However, there is a silver lining in all of this: the time they spent in the world of the dead may have brought them on the edge of awakening as Planeswalkers (substituting the single, traumatic moment that causes the Spark to ignite with a slow, painful process-- tearing away their daemons and spending time without a piece of their soul-- that drastically increases the chances of their Sparks igniting) meaning eventually, they will be together. All they have to do is find that moment of truth... and then, find each other.

But when you're a Planeswalker, the last part is almost trivial.

Oh, and the Amber Spyglass? It's an improvised Prismatic Lens.

possibly W/R.
 * Thus the great question is...are the evil angels in the series pure White, or are they like Ravnica's Orzhov?
 * Probably Monowhite, although W/B is not out of the question-- especially with Metatron. The Rebel Angels are

The Subtle Knife will return
I'm not exactly sure which law of physics this is, but I remember that "matter cannot be created or destroyed, only changed". MEANING that, somewhere and sometime in the multiverse, the Subtle Knife, which is pretty much made of Dust, which is TECHNICALLY matter, will once again be created. And someone will use it, and we will have the setting for the greatest crossover fanfic of all time.