The characters are transported by some means at the moment of the Apocalypse to the Shadow Dungeon. They fight their way out (see below for symbolism) and end up near the ruined Earth City. Here they meet different factions and characters, including Malvern. Money is useless right now- barter and favors are the only currency. They are penniless and can choose to stay in the city or leave. If they stay, they participate in trying to rebuild the city (power, water, food) and and investigate mysterious hauntings that keep cropping up. If they leave, the Ergon Scouts catch them and bring them back with the Monk's forces. Have them get captured. The Monk has foreseen their importance, but not what they would choose.
Whatever happens, the haunting mystery spans the elements as well as the spirit and physical planes. Malvern uses the party to get an exotic moss from the Shadow Dungeon which allows him to enter the Spirit World and sequester his soul in a hidden and protected place. He becomes, essentially, a lich. The characters must open the Door of Fire (they need at least one person with +10 in each of the three elements) to get to the second to bottom level of the Shadow Dungeon. In the video game, this door is open and Baird passes through to the final door (which the characters cannot pass) which requires Infusion of all three elements and the ability to progress further along the Long Road. The Shadow is the Negative Energy?
Too much interaction in the Spirit Realm draws Chaos beings, who somehow manifested along with the planes overlapping.
Symbolism:
The darkness of the beginning and having to defeat Shadow creatures and an elemental are indicative of humanity's birth into a new world because of the Apocalypse and the literal "darkness" of the unconscious and the bringing of light into dark places. Fitting as well that the mosses that grow there allow for transport to the Spirit World. Their own Shadow and ignorance brought this on, but through it they can become greater through Integration, which is the name for being Infused with all three elements. The greatest treasures are within the Shadow. Between the ape-like creatures of humanity's nature and the elemental, those are what caused the problems.
Random Thoughts:
The characters could become interested in recent hauntings (people dying imbalanced due to the element vampire) after they almost catch the murderer and see the deformed corpse. The clues from spirits eventually lead them to a portion of the city which has been displaced. Also, at first the Ergon in their party might be accepted if they continue helping, but once the Monk's forces begin to march after a few weeks, they will be detained by the powers that be. Okay, how to keep this haunting hook going? I want to combine the skills of the three Shapers. A spirit world journey by the Water Shaman where she must take a party member with her while the others defend them would be sick.
If the characters are able to choose how to deal with the spirits- the Water Shaman goes into the spirit realm and may take up to one party member (maybe this ritual gets upgraded later). He can lead them to the afterlife or bind them, allowing him to summon them at need. Perhaps some of the spirits ask for one or the other. If the Troubadour comes into the spirit realm, she can do the same. Eventually, they encounter beasts of Chaos after hearing rumor and warning of them. Ergon shamans stop going into the spirit world and the more times you enter, the more likely you are to encounter the chaos entities.
Food distribution, dealing with panic sticken people, bandits, all that comes from the chaos. After some time the the first body is discovered and the Ergon approach. Decide whether to stay in the Earth City or strike out into the wild.