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There isn't really a 'best known order' , it more depends on what faction/items you want to complete/get first, which depends on what type of character you have.
There's two conflicts that come to mind.
The first is the Fighters/Thieves guild clash. To get around this, you can either:
- Join the Fighters Guild but NOT the Thieves Guild, do the Fighters Guild quests up to the Code Book, then after getting the book from Sottilde, join the Thieves Guild, THEN give Eydis Fire Eye the Code Book.
- Join both guilds, and don't bother to complete Eydis Fire Eye's quests from the Code Book onwards. It's still possible to become head the Fighters Guild by doing this, you'll just have to get more quests from the other guild heads [i.e. the Nord in Sadrith Mora and the Orc Vivec Guilds].
If you want to become Head of both guilds, then don't side with Sjording Hard Heart in the Fighters Guild. Side with Percius in the Aldruhn Fighters Guild instead.
The second conflict is that between the Main Quest and the Tribunal Temple. Once you have visited the Cavern of the Moon and Star , then you will not be able to undertake any Tribunal Temple quests until you have progressed up to speaking with Vivec [which means becoming Nerevarine + Hortator for all the Houses + Ashland Tribes.
There is a mod that allows the player to join all 3 great houses and potentially become head of all of them, but 'technically' for RP reasons you're not supposed to be able to do this. If you're against dl'ing the mod, then I'd just be inclined to make different characters for each great house. They are meant to suit different types of character anyhow.
Apart from the Temple/Main Quest clash already mentioned, there are not any others. Whilst certain factions may dislike other factions [e.g. Mages Guild members don't like Telvanni], none of the other factions in Morrowind will prevent you from undertaking their quest lines. Chances are that as you advance to the top of each faction that everyone will love you by the end anyway.
Personally, I would start out with the main quest, as it has a pretty smooth and easy introduction compared to some of the other factions' quest lines. The Sixth House base is where it starts to ramp up in difficulty.
My personal favourite guild to complete ASAP is the Tribunal Temple, because the end reward for that happens to be a rather nice piece of Medium Armour [which I quite like, despite its' shortcomings] that is unmatched by anything else in the game. :)
Edit: One more thing! In order to become head of a Faction, you will need to train up particular 'favoured skills' to certain levels, including one that is highly trained [up to 90]. Apart from the Redoran House and the Vampire Factions , every other faction has either Short Blade, Blunt Weapon or Alteration as a favoured skill. So if you train these 3 up to 90 [and a few others to 35], then you should have the requirements to become head of [just about] every joinable faction in Morrowind!
...the role of the Camonna Tong. This comes out in the FG vs. TG conflict, but it also pertains to certain tensions that you will see within House Hlaalu. Another tension surrounds a bit of turf war concerning magic--i.e., MG vs. House Telvanni.
The game is remarkably forgiving of those who want to play multiple sides of conflicting issues--allowing you to rise to the top of rival factions (with the caveats that TFR mentions above). If you're more persnickity about roleplay stuff, though, I think your biggest questions will concern which House you'll want to join, and whether you want to mess with the Morag Tong. And if you're persnickity, you may also decline to do quests within a faction that just don't feel right. (I declined quests for Eydis Fire-Eye before I even got to The Code Book. There are other examples.)