Every normal imperial guard(not the captain or the archer, or any other imperials) attack me on sight. So do all the ordinators and high ordinators.

They dont talk to be, as soon as they see me they attack me. I didn't have any bounty, or carried any armors that could upset the high ordinators (like the her hand's armors).

It also doesnt got anything to do with downloaded mods. I didn't kill any important characters either.

So what the hell is happening here? Could it be because i am the nerevarine? That wouldn't make much sense since im a hero, not a villian.

Hmm sounds like it might be a mod conflict. Even if it doesn't seem likely it's still possible. Try disabling all the mods on your character and see if the problem is still there.

Also, Morrowind Lore isn't really the place for game bugs, moving this to Technical Support...

Hit "~" and try typing in "Player->setpccrimelevel 0" or "Player->payfinethief" that may help.

Haven’t we had this problem before? I have had that trouble myself but I have yet to come across a fix for it.

Well, new characters i made, with all the same mods as the first one on, dont get attacked by the guards

Try to implent your old savegame into the new game with the TES.
Or only the Charkter if you dont have problems with playing the game again.