As is my method, stolen wholesale from an OYT poster (phindar):
I've always liked Underdark adventures. It's a high threat, alien environment, but it's not just a dungeon crawl. It has an ecology, even if it is a mix of the natural and the fantastic. I just wrapped up a Pirates of the Sunless Sea game, and my rule of thumb on underdark ecology was to make the plants into fungi and the animals into vermin. People drank mushroom tea and herded giant beetles.
I'm a big fan of the old 1e Dungeoneer's Survival Guide and the lands of Deepearth. That's a sourcebook I've kept handy for three and a half editions and counting. In the Forgotten Realms, the only known link (I believe) between the Sunless Sea and the surface is the town of Skullport, under Waterdeep. I kept this detail for my game, and Skullport became the major importer of surface goods to the underdark; ships, slaves and wood were all brought through there by the yuan-ti merchants.
Some sites from my Sunless Sea included:
Boomtown: A fortress carved into a stalagmite island, this town got it's name from the fire giants that sold their blackpowder cannons to any who could meet their price. The refuse-filled caves under their foundry were inhabited by a clan of devious goblins (the Boomtown Rats) who stole blackpowder and used it in gourd-bombs. Boomtown also had a large (for the underdark) shantytown on the opposite side from the fire giant docks, which was a wretched hive of scum and villainy (tm).
Octopon: The mind flayer city; a sculpted island of unspeakable horrors and good bargains. Suffice to say some characters loved this place, and some never left their cabin. Octopon's "streets" are a series of canals that cut through the city. Travel is easily arranged through a great number of water taxis, although small private craft are also permitted. Octopon is pretty quiet for a city of it's size, but there are a few restaurants and alehouses that cater to visitors. (And some that cater visitors themselves.)
Nothing in Octopon is built along a straight line or a right angle. It is said that the design of Octopon is supposed to refer to a giant octopus, although if that's true it must be something that speaks to the illithid sensibilities. For everyone else, there is something disorientating about the city; visitors find it easy to get lost even on streets and alleyways they have been down several times. Sometimes when walking through the city you get the feeling being on a sharp incline or decline, even though the ground is flat. There are a few subtly curving avenues that allow you to see great stretches of the city at once, but the way the buildings seem to lean and bow in on themselves is displeasing to the visitor's eye. The city is lit by a series of braziers and street lamps that give off an uneven, greenish-blue glow. The stone of the city is carved with countless deformed and squid-like figures, as well as larger reliefs that depict odd and unsettling scenes. These carvings are everywhere, the one thing you almost never see in Octopon is blank stone.
Honzoun: The rakshasa city carved into a large, hanging stalatite; ships would dock under it and then cargo would be unloaded via levitate spells. My pc's never went here, which I thought was a shame.
Corvalag: The Duergar city of Steel and Stone. The pc's never went here either, but the ironclads and stone barges that launched from here and traveled to the duergar's mines around the Sunless Sea were frequent sights.
Sitha Igothul's Pleasure Palace: This wasn't a location as much as a large, organic structure that submerged and resurfaced at various points on the Sunless Sea. It was controlled by the underdark/undersea crime lord Igothul, a giant psionic catfish (or in D&D terms, an aboleth) and his skum assistants. Igothul kept a banquet table in his meeting room and a powerful suggestion was in effect that made anyone who entered ravenously hungry, which always freaked my players out. There was nothing wrong with the food though, Igothul just liked watching people eat. He (or really, "It") kept a number of translucent-skinned slaves around, and delighted in consuming the memories of those who had suffered greatly in unusual ways; he always payed top coin for slaves like that. Igothul was my game's Jabba the Hutt, in other words.
Stonemarsh: This was a tiny village of weird derro who kept and milked catoblepases (catoblepi?) to make into Death Cheese, which wasn't fatal but otherwise popular in the underdark. This village was eventually slaughtered by a particularly savage tribe of grimlocks (think Reavers from Serenity) who kept a derro adept who went crazy and began thinking he was a grimlock too. The party ended up here having to fight the crazed grimlocks while the derro adept kept throwing down fog clouds and silent images that not only were the grimlocks not affected by, they weren't even aware of them.
Portage: This was a locathah city on the far western edge of the Sunless Sea. The sea continued but the cave did not, and the locathah would transport ships to a sea on the other side for a price. The method was the ship was unloaded and it's crew took the cargo through caves to the other sea while the locathah scuttled the ship and swam it through the completely submerged caves. (Sailors capable of water breathing could accompany the ship, but the trip took a couple of days.) On the far side the ship was repaired the water pumped out, and could then be reloaded with its cargo.
Pellucidar: My nod to Edgar Rice Burroughs (if outright stealing can be called a "nod"), Pellucidar was a large series of caverns with a magical false sun, surface-like jungles, super-intelligent apes and dinosaur-riding Amazons. The campaign never made it that far and the world is poorer for it, but there you go.
Hellspike Prison:In my game, the Oubliette was called Hellspike Prison, a name a took from a WotC product but otherwise know nothing about. (I think it was a D&D minis terrain pack, but I'm really not sure.) In my game the Lawful Evil's had come together as the Black Sun Trading Company, and Hellspike Prison was a place they put people too dangerous to be set free but too valuable to simply kill. It was run by beholders and staffed by devils, but was otherwise the prison from the beginning of Dead Man's Chest.
Some pirate crews I used, or statted up and never used: renegade drow warlocks on the backs of huge water spiders, a longship crewed by skeletons and captained by a necromancer who specialized in cold spells, duergar ironclads, troglodyte savages in war canoes, yuan-ti on a slaver ship infested with snakes, a yuan-ti ship builti n sections that propelled itself by swimming like a snake, a host of converted Spelljammer ships (illithid nautiloids and the like), a myconid floating fortress that was itself a giant fungus, the Goblin Armada (three small rowboats), a sahaguin strike force inside of a giant zombie shark, kuo-toa who worshipped a colossal albino kraken they called Dagon, a group of ogre magi ninjas called The Oni Brotherhood, and if I dug through my notes maybe one or two more.
The subplots and deep background of my game had to do with a lost svirfneblin empire (said to be lost when the caverns flooded and created the Sunless Sea), and an ancient society of surface peoples that had fled underground and slowly been corrupted. So in addition to the usual stuff of pirates and piracy, there were also a lot of ancient temples to forgotten gods and hidden troves of the svirfs.
Hope you can find some useful stuff in all this.
As far as side routes go, if the PC's have some idea where the big bads are headed, they might be lured into taking the shorter, more dangerous route. I'm thinking something like The Descent, where the caves are narrow and constricting. Escape Artist checks (because who takes that skill?), short passages that are submerged, basically a claustrophobic nightmare. That's the underdark adventure I've always wanted to run.
And from theBlackJaw:
Cthon's advice is dead on: Treat it as wilderness instead of a dungeon. Most of it will be travel, making camp, and interesting encounters along the way... except in this case the way is a series of interconnected tunnels. You can still describe landscape, wandering monsters, trouble on the roads, etc... just describe them different.
Here is what I would do: Ask yourself who built the primairy tunnel network your players will be in. Sure large chunks might be natural cavern system, but when it comes to miles of interconnected underground roads, which most large scale D&D underdarks are, you have to imagine that one of the many inteligent underground civilizations built them at some point. Who built this one and why?
Now ask yourself who uses it now... With those to basic ideas, you can easily create a selection of interesting possible encounter locations, and descriptions of the general "wilderness terrain."
Example: In my game the underground area was built by the dwarves. It use to be Darven kingdeom, and they had miles of interconnected tunnels linking their variouis mining camps, smelting locations, temples, villages, tombs, bridges over underground rivers, and gate/guard house tunnels. Of course the dwarven civilization had been wiped out long ago, so those places were mostly ruins now inhabited by selection of underdark ecology, goblins, undead dwarves, trolls, etc.
Come up with a series of simple locations & encounters for this portion of the game that fit the theme and plot. Place the encounters on a map as if they were cities & locations on a regional map. Now draw simple lines to represent the tunnels that connect them together. The end result should look like mental map of the possible encounters locations... because it is. Now go ahead and add a note on travel time (a value in hours) to each line.
Example: In my game I placed a "bridge troll" encounter at an ancient dwarven bridge over an underground river. The dwarves had built a Tomb & shrine complex on boths sides of the bridge, overlooking the underground river space, and the resulting encounter had trolls tossing spears across the river, among other things. This site was along the path between a dwarven mining camp (goblins) and a dwarven gate house (undead). From the gate house were 3 lines (tunnels), one leading to a dead end at a strange dream temple, one leading through a puzzle encounter dealing with a damaged section or the tunnel, and another to Player's intended destination: a magic seal used to hold back an ancient evil. This was only a section of the network of tunnels by the way.
You should also come up with a few "random" or planned encounters to set in generic tunnel areas. Use this to showcase who lives down in the depths.
For example: in my game I designed some modified vermin, swarms, plants, and animals to represent the underdark ecology. In some places I had them as part of a set encounter location (and underground spring the players had to cross) and in other spots I used them as a random monster. I did save one encounter for while they made camp in the tunnels. A stamped of 6 legged wall climbing creatures... dwarven cattle equivalents gone feral rush through their campsite climbing on the floor, walls, and ceiling. As they went by a large predatory mole creature burst out of the ground... ate an under cattle creature, and then attack the party. It was an interesting encounter.
In play all you have to do describe what it's like to be traveling through the tunnel systems. How does it look, sound, and smell? Then describe every crossroads and let them pick a direction. Each path they travel is travel time. As they pass through a location, stage that encounter. Eventually they will get tired and setup camp. Treat that like they had setup camp on the side of a road on the surface.
In case your wondering, here are some more details:
Under Dark Ecology was kind of fun to design. Mostly I took existing normal monsters from the MM and added or changed them. Nothing I did changed their type from animal or vermin, and I only gave them Extrodinary abilities even if those abilities were based on spells. Had my players wanted to polymorph into a giant wasp that explodes on death in a ball of bio-luminescence, I would have allowed it.
* The dwarven 6 legged cattle were simply Bison with a crawl speed and a big racial bonus to jump. They crawled, leaped, or stampeeded along walls. They had blind sense to a short range.
* The Massive predatory moles were Dire Sharks with burrow instead of swim, and Tremor sense instead of scent. Swallow whole on a burrowing creature is interesting. I had one burst out a wall and the other burst out of the ground. The cleric used a
* I had puffball fungus growths that glowed. They were more like traps then monsters. If they took any damage (like being walked on or hit by a fireball) they exploded in a 10' burst doing acid damage. The damage wasn't much, but it did also leave biolumincent slime behind that was more or less like being hit by a Gliterdust spell (no blindness, but it makes invisible visible.) Statistically they were Small versions of a Shrieker fungus with only 1 hit point.
* I had colonies of underground flying bugs the size of dogs. I used giant wasp stats, but made them glow like fire flies (they eat the puffballs). When killed, they explode in a bright blinding flash of light (Glitterdust with blindness). Like bees attracted to an already stung aggressor, they would go into rage when they smelled one of their exploded kin... gaining a +2 bonus to attack, damage, and poison DCs against targets covered in the glowing slime of their dead kin.
* I had "Light eater beetle swarms" These were flying black insect swarms attracted to light sources. They would attack characters with light sources (torches, lanterns, glowing weapons, etc) or ignore people otherwise. The provided concealment like a fog spell in the spaces they occupied. I would add these swarms to otherwise normal encounters. Players with glowing swords had trouble, and a Goblin cleric even used a light spell to attract the swarm to the party during one fight.
Advice on underground locals: Who ever built the roads would have left signs (in their native language) carved into them... which makes crossroads easier to understand. Who ever uses the roads and locations these days would leave graffiti scrawled all over these crossroads, this can be used to hint at which way the PCs should or should not go... such as were some big nasty kyber monster lives.