Last updated 5-21-17
Quest 1) The Dissident Priests send a dream sending to the player, asking them to return to Holamayon (Use the same coding as the Dagoth Ur sendings). Once in Holamayon, the Priests say they are now turning their attention to building the New Temple Order, and ask the player to go to Simine of Necrom as a possible candidate to kick things into order, who they hear has been starting to question her faith.
Alternatively, Temple members receive a courier from Alvu Sareleth, the Matriarch of Necrom, who says she is worried Simine is losing her way, and wants the player to check in on her.
Either way, the player is then to speak to Simine. Simine says she is worried about a group of Ordinators in Mourning who went out to deal with some troublesome Ashlanders and never returned. She asks the player to check on them for her. At this point, the player can either return to Alvu, or go find the Ordinators. If the player returns to Alvu, she asks the player to go ahead and find the Ordinators anyway, "if it it will help put SImine's doubts to rest".
Quest 2) The player finds the Ordinators who have been holed up in Drakehold. They are reluctant to speak to the player and seem extremely jumpy, but after a little persuading, the following story comes out: The Ordinators were officially sent to deal with some Ashlanders who were part of the Nerevarine cult and becoming increasingly aggressive. Though the confrontation with them was meant to be peaceful, it got out of hand, with either the Ashlanders or the Ordinators picking a fight (it isn't clear which; different Ordinators will say different things), and the Ordinators ended up killing all the Ashlanders. The ancestor spirits are now angry and have been making their displeasure known to the Ordinators through whisperings and dreams.
The player can convince the Ordinators to return to Necrom to face justice, to flee, or to take justice into their own hands and kill them all (Mephala, 1 point), or to convince them to renounce their faith in the Tribunal (Boethiah, 1 point).
Quest 3) The player returns to either Simine or Alvu once they are done dealing with the Ordinators. Both questgivers are disturbed by this turn of events, and decide that something must be done about the waning faith in the Sacred Lands. They decide to summon Alandro Sul and try to get out of him for once and for all the story about what happened under Red Mountain.
Simine's perspective: For years Simine has assumed the Ashlander tradition was just a bunch of nonsense, but with the return of the Nerevarine, she is now starting to wonder otherwise. She wants to summon Alandro Sul to get the full story "from the mouth of the horse".
Alvu's perspective: Alvu has been getting increasingly angry with the questioning of the Tribunal. She wants to summon Alandro Sul to disprove the Tribunal's guilt in murdering Nerevar: it's intentionally unclear if she really wants to listen to what Alandro Sul would have to say, or just find a way of silencing or coercing him to say what she thinks the Temple needs to hear to maintain their faith.
To summon Alandro Sul, the player needs to find some ringlets of his legendary Wraithmail, which are traditionally held by Ashlanders. There will be four rings in all to obtain. The quests for these will symbolize the House of Troubles.
Summoning Peakstar) As the rings are known to be kept among the Ashlanders, the player needs spiritual guidance from an Ashlander ancestor. Peakstar is in a unique position because she is an Ashlander ancestor ghost and a Nerevarine, and as such conneted to both the player and Alandro Sul in a very special way. This quest would be doing the ritual to summon her (should be a somewhat grand and involved affair).
When summoned, Peakstar gives the player the location of one ringlet, while saying the other two Good Daedra know the location of two others. She tells the player they must please the Daedra through their actions while obtaining this ringlet (aka, a total of 2 favor points). If the player fails, the Daedra themselves scolds the player when they try to call on them, and tells them they must go through an Imperial Oracle instead. (Ex: "You think," the voice of Boethiah rung out, "that you deserve help? I think not! I do not care for your quest, and you have done nothing to make you interest me, %PCName. Why don't you crawl on your belly to the Empire of Man and beg for their scraps of help?" And the player does just that. ) The Imperial Oracle's questline is a matter of getting Cyrodilic herbs for the Oracle's ritual, then waiting 7 days for the Oracle to get a vision.
As well as the quests in this line, the player has three other methods of gaining favor: completing the artifact quests will get +1 favor with the respective Daedra, being a part of the Morag Tong will earn +1 favor with Mephala, and killing Vivec will gain +1 favor with Boethiah.
Malacath's Ringlet Quest) As the player may have already gotten this ring, this quest can be done at the same time as the Summoning Peakstar quest. Malacath's ring lies with the Ordinators of Mourning, who took it from the Ashkhan of the tribe they murdered. This Ashkhan has Sul as part of his name. How the player obtains this ring is up to how they dealt with the Ordinators. (If the Ordinators faced justice, then one will give the ring to the player in thanks for helping them retain/regain their honor. If all slain, it is found on the leader's corpse. If they renounced their faith or fled, they give (gave) the player the ringlet so that Alva does not hunt them down later on.)
Molag Bal's Ringlet Quest) Peakstar gives the player the location of this ring once she is summoned. This ringlet is in the hands of an Imperial Cultist, well known for both collecting historical artifacts and being a fairly corrupt individual (something to do with sexing up the local girls might be in order, considering Molag Bal's influence...). This Imperial Cultist is well established in their town, but now find their position being threatened by a newcomer, a firebrand coming from Cyrodiil who is doing their best to convert Dunmer to the Nine Divines in light of the Red Mountain crisis.
The firebrand is on to the Cultist and his corruption. The Cultist knows this, and asks the player to steal the evidence and use it against the firebrand instead. The player can  incriminate the firebrand as asked (both)  refuse to help which means the Cultist goes to jail (neither)  break into the firebrand's place to erase the evidence, meaning neither get in trouble (Mephala)  convince the Cultist to confess, which would get both in trouble (Boethiah). Confessing could be roleplayed as either the player trying to bring the Cultist to divine forgiveness or as the player intentionally getting rid of both characters.
, , and  ends in the Cultist giving the ringlet to the player as a reward.  results in the player needing to take the ringlet from the Cultist's belongings after he is jailed. If at any point the player kills one, both Daedra approve. If the Cultist is the one killed, just like in  the player will then need to take the ringlet from his belongings.
Sheogorath's Ringlet Quest) Mephala, who governs secrets and lies, shows the player to this ring. This one lies is in the hands of an eccentric traveling priest who supposedly doesn’t know the worth of what they’re carrying. When the player talks to him, the priest speaks in vague terms about his guilt over killing someone dear to him, and the player must help him absolve his guilt over this before he will give them the ring. This old priest is in actuality an avatar or echo of Seht/Sotha Sil talking about his guilt over Nerevar’s death, though this should be kept obscure.
Mehrunes Dagon's Ringlet Quest) Boethiah shows the player to this ringlet. The player should also get to see the Nerevar bonewalker uttering meaningless platitutes to the Tribunal as part of this.
The player must obtain a ringlet from an ancestor spirit who is already dead and had its remains sent to the ghostfence machine. This spirit was half-processed, but then the Nerevarine killed Dagoth Ur, rendering the Ghostfence and further processing unnecessary. It is now half-mad and wants to be free. The player could  complete the processing, which implies further rendering of it into pieces so it is "destroyed",  just release it, which would make the Necrom priests angry and the spirit would probably attack the player or otherwise cause havoc on the way out as it's half-mad, or  take it to its family's tomb.
If the player chooses , they must coax the spirit into entering an urn. Angry spirits spawn for as long as the player holds the urn. The player may choose to go back and do either  or . Once the player gets the half-mad spirit to the tomb, the family does not want it there. The player must then either convince the family to keep it, or release it across the Eastern Sea, to follow Veloth.
Upon agreeing to do one of these choices, the spirit gives the player its memory of where the ringlet is, in the family tomb. If the player convinced the family to take in the half-mad spirit, then they allow the player into the tomb peaceably.
Quest 9) The player obtains the final ringlet. Eagerly, the questgiver begins the ritual to summon Alandro Sul through them, using the ghostfence machine room as the site of the ritual. She is interrupted by Erendes Hlervan, who says they are committing a terrible heresy, and it is his duty to put a stop to it. This scene is to be voiceacted. Somewhere in here it should also be discovered that the Nerevar bonewalker has disappeared.
Erendes's perspective: Erendes serves as a counterpoint to Simine's doubt and Alvu's willingness to break the rules. Whereas the ordinary Ordinators have become afraid and uncertain, he remains resolute in his faith. Whereas Alvu and Simine want answers (if for different reasons), Erendes would confront them with the idea that they are better off not knowing.
After Erendes is dealt with, the ritual to summon Alandro Sul is finished. Each ringlet speaks with fragments of Alandro Sul’s voice, giving clues to the location of the holy relic and how to get to it. As each ringlet is understood to be an influence of the House of Troubles, each clue has to do with the Bad Daedra.
Quest 10) The relic is a hidden antechamber in the Necrom catacombs. The chamber holds the Foul Murder mural, a painting created during the Red Moment, which cannot be destroyed, instead disappearing and reappearing in another location if someone tries to. The Tribunal finally managed to enchant it to lock it away under Necrom.
When the party enters the chamber, everyone stands goggling at the mural. There is a sound, and all turn around to see the Nerevar bonewalker floating on up to the Nerevarine. The bonewalker touches the Nerevarine. Cutscene happens--like the one that starts the game, it should be a bit jumbled and symbolistic rather than seeing any particular thing, to convey the feeling of the player receiving a lot of information all at once. Then the cutscene ends the player is forcegreeted by one of the NPCs, asking the player WTF just happened, that the player had lost consciousness, and the bonewalker turned to dust.
The player can then turn to Alvu or Simine (whoever is present), and recount what happened at the Battle of Red Mountain through a series of dialogue choices. This should serve as the player choosing which version of the canon they want to be true for their character, such as: that Nerevar was murdered for the Tribunal's personal gain; that Nerevar was murdered because the Tribunal truly thought that would be best for their country; that Nerevar was killed in battle and the Tribunal made the best of a bad situation; that the Nerevarine is not truly Nerevar and just happened to fulfill the prophecies; or my personal favorite, that perhaps Nerevar asked the Tribunal to do it, seeing glimpses of what would happen thanks to Azura. Other popular fanon versions could be added here as well.
Picking one of these stories (or offering all of them as food for thought) would finish the quest. The questgiver would react to these tellings as befits their personality, including stepping down from their post or going on a murderous rampage. If we wanted to be ambitious, we could also change various pieces of the dialogue all over Morrowind to lend credence to whatever version of the story the player picked.