Lots of talk about planar cosmology here, so I'll put in some stuff that I left out last time:
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The Inner Planes are surrounded and contained by the six elemental planes. Of these, the four classical elements act as passive "walls", but the positive and negative elemental planes serve a greater role. New planes are spontaneously generated by the positive elemental plane, and over time will tend to drift towards the negative elemental plane and oblivion. Conditions on each plane will reflect where along this process the plane is; those close to the positive energy plane will be idyllic paradises, and those close to the negative energy plane will be barren, apocalyptic wastelands. Cause and effect are difficult to separate, as events within each plane can cause it to move "up" or "down", or movement up and down can trigger good or bad events in the plane. In any event, salvation, elevation, and ascension of the entire world IS possible (through massive, worldwide goodness), and most religions have this truth at their core. However, most religions do NOT release this knowledge beyond their inner-most circles, because enlightened self-interest just isn't enough.
Outer planes are simply entire planes, or parts of planes, that have been ripped out of this natural state and placed beyond the rules of buoyancy and sinking by beings powerful enough to be called gods.
Upon death, a soul leaves the world and naturally floats either upwards towards the prime elemental plane, or downwards towards the negative, depending on its alignment. (Neutral alignments will still drift one way or another, but much more slowly.) Souls that eventually reach the positive energy plane become one with life and goodness itself, and have a hand in crafting entire new planes as Creators. Souls that land themselves in the negative energy plane are consumed by oblivion in a suitably horrific manner. However, MOST souls would tend to hit another material plane before their journey is complete, causing them to be reborn in a better, or worse, place. Also, the gods like to grab souls in transit and bring them to the outer planes. While there is competition for souls, belief and alignment give critical advantage, with the result that souls usually get grabbed by the pantheon they believed in and by a deity suitable to their alignment and placed in an afterlife suitable to their belief system.
Movement between material planes by mortals was usually accomplished via the Plane of Twilight. Though navigating that plane is normally extremely hazardous and chancy, conduits linking pairs of planes made interplanar travel accessible even to the least powerful of individuals. No great magic is needed to use conduits, just a good map or perhaps a high Magoo factor. Naturally occurring conduits are dangerous and unpredictable, often encountered in storms or other chaotic circumstances, but many of the extraplanar races learned how to forge their own artificial conduits. These conduits tended to take on different flavors, depending on who made them, which is why (for example) elven conduits tend to be experienced as aquatic journeys.
A great interplanar confederacy known as Fae'rin was established this way. Though principally comprised of fey, most races were either full members of the confederacy (gnomes and halflings), or within its sphere of influence through trade and cultural exchange (dwarves, elves, and goblinoids) or colonization (humans). (This is why the only language that humans speak is Fae'ri Common. When your tribe has its own native tongue, and the tribe over the hill has a different native tongue, but you both speak Common because that's what the Fae'ri who want to trade you jewelry for spices speak, pretty soon all humans are speaking Common to each other.) The fall of the goblinoids and the resultant bloodshed (known as the Goblin Wars) sweeping across the planes led to the collapse of Fae'rin, as some worlds were overrun, others destroyed the conduits to threatened planes, refugees trapped in sinking worlds were twisted and desperately sought escape through any means possible, and free travel between the planes became chancy and dangerous. What conduits remain are often hazardous and ill-maintained, and used only by medium-or-high-level characters.
Something in the Plane of Twilight was altered concurrent to the Goblin Wars, and it has become a much more dangerous and darker place. Competing explanations by planar scholars have been provided (including who is to blame), but no one theory is dominant. This further impeded travel after the end of the Goblin Wars. The Plane of Twilight is now more commonly known as the Plane of Shadows.
Time proceeds differently on different planes, but from the human plane the Goblin Wars started about 2500 years ago. They rather quickly fell on dwarven and elven civilization. The home elven plane was first invaded about 2300 years ago, and finally fell about 2000 years ago. The dwarven plane fell in about the same time frame. The goblin hordes reached the human plane about 2200 years ago, but this was an auxiliary thrust. The goblinoids were focused on the dwarves, elves, and Fae'rin, and weren't particularly interested in the primitive humans. (This means that the human plane only got twenty or so legions of goblinoids securing it, rather than being overrun entirely.) The Goblin Wars never really ended, but the invading hordes lost most of their momentum and coherence about 1800 years ago. An enslaved humanity began throwing off their shackles about 1500 years ago, this marking the rise of the Twins, and can be properly said to have dominated their plane about 800 years ago. This empire lasted and expanded until about 300 years ago, when it collapsed under the weight of its bureaucracy and internal feuds. The culture and Church still remains intact, but politically it has splintered.
.... also, I forgot to mention. The Human Empire, though dominant in the plane until its collapse, never totally converted all of humanity. Uncivilized humans on its fringes still worship a combination of natural elements and the other-worldly Fae'ri, and comprise about a third to a half of all humanity. I could give the barbarian humans a pantheon as well, or just say it varies by tribe.
Okay, enough and more-than-enough planology and history. Onto responses!
Humans:
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I'm agreeing with Vitruviansquid -- once I've got the basic idea of what the human gods were elevated for, I need to abandon the idea of a religion based on portfolios and focus on a religion based on their human personalities, desires, and interests. Human gods will be PEOPLE, with all the complications and curlicues suggested by this.
Kitten Champion: All interesting ideas, but they interfere somewhat with stuff I've already got planned. Let's see what I can incorporate...
What I had: The Twins were definitely humans. They learned various arts from the dwarves and elves, and brought them back to their own kind to form the basis of civilization. They were captured, tortured, and executed by a union of savage races trying to squash the upsurgent human "rebels", but in the process they were turned into martyrs and the seeds of human civilization were thrown into a fanatic fervor that turned the tide of the war and broke the power of the savage races.
Now: The dwarves and elves were in trouble. Though their colonies and subterranean cities were very secure, the rest of the plane was overrun by goblins, and other races twisted into savagery by the sudden falls of their home planes (orcs, gnolls, etc). They sought to build the much-more-populous humans (who at the time treated the other races as otherworldly spirits rather than enemies) up as allies and proxies, and turn them against the savage races. I don't see them assassinating the Twins at the moment when it looked like the savage races would win, but perhaps they failed to show up with their armies in support of what looked like a failed gambit. This earned those two races the distrust of humanity, but they're still pretty far down on the list of grudges to settle, and in the meantime trade, wary coexistence, and temporary alliances against mutual threats are the norm.
Also, I see humanity as taking the initial gifts of the dwarves and elves as being somehow polluted of inferior, and making it imperative to produce a superior HUMAN art as soon as possible. Thus, while dwarves taught humans the art of perfectly cutting and shipping stone so that they fit together to form a fortress that needed no mortar, elves taught them the lore of gathering and nurturing edible plants, these were "improved" upon by reinforced concrete and intensive farming that exhausts the land. The stalwart dwarves have been known to shed a tear or two as they watch perfectly good granite being ground down to concrete and bagged for shipping, and the elven opinion of high-yield farming is hardly repeatable.
The Human Pantheon is definitely going to be a united force. There might be some competition within it, but it will be less a matter of holy war and more a matter of court politics. I don't think that your Storm of Souls is a good fit for it, but might work well in the Elven, Halfling, or Goblinoid religions.
I also kind of like the idea of the cycle of rebirth, but I'm aiming for more of a feudal European than south-east Asian feel for humans. I'm thinking that all humans are pressed into service of humanity and the Pantheon in the afterlife, and their rank in the afterlife is dependent on their accomplishments in life. Kind of a Valhalla, only with much more going on than just drinking and fighting. However, any soul may petition for rebirth, in hopes of improving their position the next time around.
Also, I can't believe I didn't see this earlier, but human religion has to be horribly entangled with a guild structure. The smith's guild is not JUST a guild, it's also the Church of the Blacksmith. This suggests severe curtailment on social mobility, especially with a secular law (imposed well after the religion was founded) saying you inherit the profession (and faith) of your family. One can move up and down in the Guild easily enough, but moving SIDEWAYS to another Guild... and essentially changing churches... has a lot of obstacles involved. Furthermore, as new arts are invented, the established guild-churches eagerly snap them up, claiming they fall under their purview, while the new artisans clamor that this is a new art and deserves to be a new guild, with the inventor elevated to godhood. All of this is made worse by the prospect of an afterlife of basically performing the same art you did all your life. Someone who hates their job while alive isn't going to want to do it for eternity. This has spawned several doctrinal debates... is it the will of the gods for someone who was born in a blacksmith family to remain in the blacksmith profession? Can someone be reborn into a different profession, or always just the same one? The power and purviews of the guilds are multi-faceted. Larger guilds with a wide variety of arts in their portfolios have vast income and worldly power, offer a wide choice of professions to their members, and provide their gods with lots and lots of worshipers. Smaller guilds... don't. Meanwhile, there may be cults within the guilds, who never accepted their art's absorption into the larger guild, and heretically worship that inventor in secret.
I don't see pulling off the Twins as elves. Official theology will have them being humans or aasamir. However.... I COULD buy into the idea that they were half-elves. This dovetails well with the preexisting notion of other races as powerful spirits, and could easily have been turned into half-angels in the retelling. I don't think an "official" stance on this is necessary. Instead, we've got a few elves somewhere spreading that rumor and earning the hatred of humans, and more progressive (less bigoted) human priests suggesting the possibility and being branded as heretics by their conservative brethren.
The Twins Themselves, I see as caught in something of a bind. In life, they nurtured and harnessed human bigotry as a liberating force (the only good orc is a dead orc!). In godhood, they've become aware of both the nature and history of the planes, and know that if humanity runs full tilt into pogroms and purges it could mean the twisting and corruption of their world. This could be another Goblin Wars in the making. However, the Twins are dependent upon their worshipers for power, and the religion had taken on a life of its own before the Twins could really settle into a stewardship role. They're afraid of moving too quickly, making too many contradictory or confusing revelations, for fear that humanity will splinter in the face of the other races, the faith-power feeding the Twins' godhood will slack off, or that the church will shatter (and with it, their ability to disseminate their gradualist instructions). And, of course, the Twins ARE products of their times, when the only good orc WAS a dead orc, and they have the prejudices to match.
Dwarves:
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I'm liking what several posters have said: The Inner Sun was the original god of the religion, it got transformed into the Inner Light path of enlightenment (which can have some real-world Taoist or Confucian elements) for practical reasons. The Inner Light is by far the dominant religion of those dwarves who haven't wandered back down their tunnels on pilgrimages and DIED HORRIBLY, but the Inner Sun still exists and regards the other dwarves as heretics. Also, there have been several teachers regarding the Inner Light, and the religion can be divided into different schools of thought. Those teachers HAVE become gods in the sense of power, but unlike most gods don't present themselves as such, and they are more interested in guiding the souls of dwarves to the positive energy plane than to an artificial afterlife. Regardless of school (or original sun-worship), if they're good dwarves their afterlife is to become One with the Light/Sun, joining their ancestors. The Light (or Sun) can additionally be a metaphor for inspiration. I like the idea of creativity and crafting being an act of worship (and even divine mission); all this dovetails well with the role of the positive energy plane in my cosmology. It also suggests the possibility of an "outer darkness" to balance it, but I think I should find a different name for that to avoid treading in real-world religion.
Elves:
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I'm thinking the elven court under the Last Emperor needs to be deified as well. However, each colony was supported by a different Patron in the court, and will thus worship that individual principally. I also like the idea of the ship's Captain being the primary object of worship; the Court was at a distant remove, and dealings with it could only be accomplished via the Captain. In actual history (which take longer to die out, given elven lifespans), the bodies of elves were ferried back to the home plane to be placed in state; in the new mythology, the Captain ferries the souls of the dead to the Court. (I like how this works vis-a-vis Tolkein's "go west beyond the sea" business.) In the mythology, the Court is a place of delights, where all the exotic wonders brought home by colonies of a thousand different specializations are enjoyed, and all elves are united as one race.
.... which just leaves me the question of what the elves USED to believe, and how the older generations regard this new heresy. Maybe the Storm of Souls works here.
Gnomes:
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I'm not going with the idea of the lurking evil, but I think the planology I presented above makes for a good substitute. I'm also thinking that while they will acknowledge "gods" of all sorts of animals, they are particularly found of the burrowing mammals that they can talk to. Laughing Fox, Wise Mole, Grumpy Man Bear. I was thinking more of a native American folklore, but Joe the Rat's idea of sacred sites and Shinto elements is also intriguing, and I'm wondering about fusing the two.
Halflings:
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I'm liking Joe the Rat's ideas, except for one thing: All the old gods that halflings worshiped (and still worship) on other planes STILL EXIST. In their original form. Because there ARE the more traditional hallfings out there, still worshiping.
This has me wondering, to what extent does worship shape the god, and to what extent does the god shape worship? Suppose that the exiles, through spreading out to all the worlds they could reach, began to outnumber the stay-at-homes? Suppose that conservative halfling faith was overwhelmed by the worship of the rebellious? Could the gods themselves be twisted by that change?
Right now, I'm seeing every god in the Halfling pantheon as having an Old and New face. The Old Face is the traditional view (the one of the domestic halflings), and the New Face is the view of the halflings who've gone abroad. In essence, each god is a duality, having a good and evil side. The New Faces could be very, very much as Joe the Rat describes. We can even have a sort of expected transition from New Face to Old, where as a halfling (reluctantly) matures, she becomes more amiable to the Old Faces. There might even be an Age of Geezerhood (or something like that) where the halfling is EXPECTED to start worshiping the Old Faces over the New. Don't trust anyone over 30, dude, they all worship the Weaver and Gaoler.
Goblinoids:
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Greco-Roman goblinoids.... actually works, with some slight modifications. Emphasize these gods at their most boorish, petty, and spiteful, then shift some greater gods to lesser status and lesser gods to greater status. An Ares-equivalent could become the head of the pantheon, while the Zeus-equivalent could be just a major god. Demeter might be reduced to minor status and Nike promoted to major, and so on. That's the sort of transition that could be made when the goblins fell. I think the Greek gods make a good template, and feel but I'd definitely want a different pantheon, not just "Oh lookie greek gods".