SilverJakler

Psst... go to the giant black castle that you need to go through a maze to get to. It's directly South of Agate City, which is at the eastern end of Route 1.

Ok, so you have the following things left to happen (I'm positively sure I'll forget something, but oh well):

1-Battle Cain

2-Encounter with El and Luna's getaway

3-Gossip gardevoir "joins" El

4-You get to the inside of the great door that connects route 1 with the city

5-Radomus, Cain and you have an epic encounter against El on an underground zone dedicated to arceus.

6-You finally access the city from the grand gate, and it remains open fro...

...m that point onward.