So today, I was playing morrowind and I thought I was still on the main quest, then everything changed I joined the mages guild, went to full rank and it broke the main off, and it takes me close to the end of the game, does anyone know of this?

You can't advance the MQ through the Mages Guild. What was the last thing you did for the MQ? Hortator? Neverarine? (SP?) Have you met a certain deity yet? or the other one?

You mean the "kill the councilors" quest? That kills master Aryon who I think is essential for the MQ (and, of course, the Telvannis). I've never done that quest because I always kill Trebonius first but I thought that you only get the quest if you have completed the MQ. Maybe the side path will allow you to complete the MQ.

You sided with the biggest idiot in Vvardenfel? Never side with Trebonius, his mere presence represents an accident waiting to happen.

I just beat the mage's guild and im already at the end of the game, this make's no sense to me at all, because I was only on the part where you have to find the cube, I just restarted it and it took me to the end of the game, I don't understand how this happened!

I'm not sure what you mean. Exactly what happened that makes you think you're at the end of the game? You haven't found the cube yet?

In my journal it tell's me that I have to fight dagoth ur, I don't understand how this happen, im just going to restart a new game i'm quite confused.

This is very odd. Are you over level 20 and do you have at least 50 reputation? You may have triggered the side path where Vivec asks you to kill Dagoth Ur without doing the Hortator stuff. In this case, though, you should have been asked to go to visit Vivec.

It's my journal, it like bugged itself, I don't know I can't really explain this.