heres my idea
Link travels back to Termina many years later (or as a different link) the one door in the Clock tower shuts on him again but this time their are four indentations in it. Link finds out that the doors will open when the flow of water comes back so he goes to four temples around Termina where he meets a fairy after defeating a boss and gets a element ( one of the four elements from MC)then the fairy makes water flow back through that area of Termina. After he gets the fourth a bunch of shadow Links appear and they take the elements and a mask that you cant see very well (majora's mask; you are in Stone Tower Temple for this part). They use them to open the door and then close it behind themselves. Link then finds out the only other way to open the door would be to awaken the four giants from the four temples. So Link goes to the four temples from MM but the temples look different from time. Link eventually gets through the door where he travels and finds out they remade the Twilight Mirror and went to the Twilight Realm. Link goes there and finds out they were the original twilight people. Midna tells then that they arent welcome then Link defends her and defeats the what looks like head of the Shadow Links. In shadow Links dieing words he says well their master will take over the kingdom or something so Link rushes to Hyrule Castle where he meets the leader who is wearing a robe and is looking away from Link. The leader takes off its robe and turns around to find out it is Majora and Majora says something then the battle happens. Link wins and both Termina and Hyrule are peaceful again. During the credits you see that part of the forest has been moved and a path has been made between Termina and Hyrule and that people are traveling back and forth down it.
This would be my storyline
Yeah Interesting Idea .... Maybe we could use a bit of it

I don't know whats happening with the story right now. We also have one more to work with.
But thanks for your thoughts.

I'm thinking the main story in hyrule so we will see......
Here is a little update on the link model.
What do you think ? Should the colors be different ?
What about the resolution of the model(I try to keep it low as possible, almost nintendo 64 style, but much cleaner) .....